Read summary

Alignment summary

Reference genome alignment statistics. These were generated using seqkit ) `seqkit bam -s`
sample_id PrimAlnPerc MultimapPerc PrimAln SecAln SupAln Unmapped TotalReads TotalRecords
sample01 100.0 0.0 218 0 0 0 218 218
sample02 100.0 0.0 229 0 0 0 229 229
sample03 100.0 0.0 206 0 0 0 206 206
sample04 100.0 0.0 193 0 0 0 193 193
sample05 100.0 0.0 168 0 0 0 168 168
sample06 100.0 0.0 195 0 0 0 195 195

Transcriptome summary

Transcriptome summary
Total genes 13
Total transcripts 15
Max trans. len 2608
Min trans. len 324
Transcriptome summary
Total genes 13
Total transcripts 15
Max trans. len 2608
Min trans. len 324
Transcriptome summary
Total genes 13
Total transcripts 15
Max trans. len 2608
Min trans. len 324
Transcriptome summary
Total genes 13
Total transcripts 14
Max trans. len 2611
Min trans. len 327
Transcriptome summary
Total genes 15
Total transcripts 17
Max trans. len 2609
Min trans. len 312
Transcriptome summary
Total genes 15
Total transcripts 16
Max trans. len 2609
Min trans. len 312

Annotation summary

The following plots summarize some of the output from gffcompare
  • Totals: Comparison of the number of stringtie-generated transcripts, multiexonic transcripts and loci between reference and query
  • Performance: How accurate are the query transcript annotations with respect to the reference at various levels
  • Missed: Features present in the reference, but absent in the query
  • Novel: Features present in the query transcripts, but absent in the reference

Query transfrag classification

Summaries of the classes assigned by gffcompare, which describe the relationship between query transfrag and the most similar reference transcript. This diagram illustrates the different classes.
Class Count Percent Description
i 4 26.67 intron
= 4 26.67 complete
x 3 20.0 exonic
k 2 13.33 containment
o 1 6.67 overlap
s 1 6.67 opposite
Class Count Percent Description
i 4 26.67 intron
= 4 26.67 complete
x 3 20.0 exonic
k 2 13.33 containment
o 1 6.67 overlap
s 1 6.67 opposite
Class Count Percent Description
i 4 26.67 intron
= 4 26.67 complete
x 3 20.0 exonic
k 2 13.33 containment
o 1 6.67 overlap
s 1 6.67 opposite
Class Count Percent Description
x 5 35.71 exonic
i 3 21.43 intron
u 2 14.29 unknown
= 2 14.29 complete
o 1 7.14 overlap
s 1 7.14 opposite
Class Count Percent Description
i 4 23.53 intron
x 3 17.65 exonic
s 3 17.65 opposite
= 2 11.76 complete
u 2 11.76 unknown
k 2 11.76 containment
o 1 5.88 overlap
Class Count Percent Description
i 4 25.0 intron
= 3 18.75 complete
s 3 18.75 opposite
u 3 18.75 unknown
x 2 12.5 exonic
k 1 6.25 containment

Isoforms

This table details each isoforms identified per sample. Table interactivity can be slow if too many isoforms are loaded. The number of isoform rows to load in this table can be set with isoform_table_nrows. It is currently set to 5000.
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
TARDBPP1 ENST00000442013.1 x sample01_batch_1.5.1 2 5 2589 sample01 3.0
TARDBPP1 ENST00000442013.1 k sample01_batch_1.4.1 2 8 2610 sample01 3.0
TARDBPP1 ENST00000442013.1 = sample01_batch_1.4.2 1 0 1203 sample01 3.0
TPM3P2 ENST00000397772.2 k sample01_batch_1.9.1 3 8 2058 sample01 2.0
TPM3P2 ENST00000397772.2 s sample01_batch_1.8.1 3 12 2067 sample01 2.0
RPS4XP2 ENST00000458402.1 o sample01_batch_1.1.1 2 3 814 sample01 2.0
NCOA5 ENST00000290231.9 i sample01_batch_1.11.1 2 44 326 sample01 2.0
NCOA5 ENST00000290231.9 i sample01_batch_1.10.1 2 3 360 sample01 2.0
RPS4XP2 ENST00000458402.1 = sample01_batch_1.1.2 1 0 793 sample01 2.0
ITCH ENST00000374864.7 i sample01_batch_1.13.1 1 69 571 sample01 1.0
RP5-836E8.1 ENST00000400616.2 x sample01_batch_1.2.1 1 12 1308 sample01 1.0
SF3A3P1 ENST00000446317.1 x sample01_batch_1.3.1 2 3 362 sample01 1.0
ZNF337-AS1 ENST00000428254.4 i sample01_batch_1.7.1 2 3 1457 sample01 1.0
RPL15P1 ENST00000439981.1 = sample01_batch_1.6.1 1 3 600 sample01 1.0
RPL12P4 ENST00000432629.1 = sample01_batch_1.12.1 1 3 497 sample01 1.0
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
TARDBPP1 ENST00000442013.1 x sample02_batch_1.3.1 2 6 2589 sample02 3.0
TARDBPP1 ENST00000442013.1 k sample02_batch_1.2.1 2 8 2610 sample02 3.0
TARDBPP1 ENST00000442013.1 = sample02_batch_1.2.2 1 0 1203 sample02 3.0
TPM3P2 ENST00000397772.2 k sample02_batch_1.9.1 3 8 2058 sample02 2.0
TPM3P2 ENST00000397772.2 s sample02_batch_1.8.1 3 12 2066 sample02 2.0
NCOA5 ENST00000290231.9 i sample02_batch_1.12.1 2 6 360 sample02 2.0
NCOA5 ENST00000290231.9 i sample02_batch_1.13.1 2 50 326 sample02 2.0
RPS4XP2 ENST00000458402.1 = sample02_batch_1.1.2 1 0 793 sample02 2.0
RPS4XP2 ENST00000458402.1 o sample02_batch_1.1.1 2 2 814 sample02 2.0
ITCH ENST00000374864.7 i sample02_batch_1.10.1 1 69 571 sample02 1.0
RP5-836E8.1 ENST00000400616.2 x sample02_batch_1.4.1 1 16 1308 sample02 1.0
ZNF337-AS1 ENST00000428254.4 i sample02_batch_1.7.1 2 3 1457 sample02 1.0
SF3A3P1 ENST00000446317.1 x sample02_batch_1.6.1 2 4 362 sample02 1.0
RPL12P4 ENST00000432629.1 = sample02_batch_1.11.1 1 1 497 sample02 1.0
RPL15P1 ENST00000439981.1 = sample02_batch_1.5.1 1 1 600 sample02 1.0
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
TARDBPP1 ENST00000442013.1 x sample03_batch_1.3.1 2 4 2601 sample03 3.0
TARDBPP1 ENST00000442013.1 k sample03_batch_1.2.1 2 8 2610 sample03 3.0
TARDBPP1 ENST00000442013.1 = sample03_batch_1.2.2 1 0 1203 sample03 3.0
NCOA5 ENST00000290231.9 i sample03_batch_1.11.1 2 8 360 sample03 2.0
TPM3P2 ENST00000397772.2 s sample03_batch_1.8.1 3 14 2066 sample03 2.0
TPM3P2 ENST00000397772.2 k sample03_batch_1.9.1 3 3 2058 sample03 2.0
NCOA5 ENST00000290231.9 i sample03_batch_1.12.1 2 42 326 sample03 2.0
RPS4XP2 ENST00000458402.1 o sample03_batch_1.1.1 2 1 814 sample03 2.0
RPS4XP2 ENST00000458402.1 = sample03_batch_1.1.2 1 0 793 sample03 2.0
RP5-836E8.1 ENST00000400616.2 x sample03_batch_1.4.1 1 10 1308 sample03 1.0
ITCH ENST00000374864.7 i sample03_batch_1.13.1 1 62 571 sample03 1.0
SF3A3P1 ENST00000446317.1 x sample03_batch_1.6.1 2 3 362 sample03 1.0
RPL15P1 ENST00000439981.1 = sample03_batch_1.5.1 1 4 600 sample03 1.0
RPL12P4 ENST00000432629.1 = sample03_batch_1.10.1 1 4 497 sample03 1.0
ZNF337-AS1 ENST00000428254.4 i sample03_batch_1.7.1 2 3 1457 sample03 1.0
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
TARDBPP1 ENST00000442013.1 x sample04_batch_1.2.2 2 3 2613 sample04 3.0
TARDBPP1 ENST00000442013.1 o sample04_batch_1.3.1 4 1 1903 sample04 3.0
TARDBPP1 ENST00000442013.1 x sample04_batch_1.2.1 2 4 2611 sample04 3.0
CDC42P1 ENST00000456658.1 x sample04_batch_1.11.1 1 32 1406 sample04 2.0
CDC42P1 ENST00000456658.1 = sample04_batch_1.12.1 1 0 548 sample04 2.0
NCOA5 ENST00000290231.9 i sample04_batch_1.10.1 2 3 329 sample04 2.0
NCOA5 ENST00000290231.9 i sample04_batch_1.9.1 2 20 357 sample04 2.0
RP5-836E8.1 ENST00000400616.2 x sample04_batch_1.4.1 1 13 1899 sample04 1.0
TPM3P2 ENST00000397772.2 s sample04_batch_1.6.1 3 7 2066 sample04 1.0
CBFA2T2 ENST00000375279.5 i sample04_batch_1.7.1 2 3 345 sample04 1.0
ADA ENST00000372874.7 x sample04_batch_1.13.1 3 2 634 sample04 1.0
FTLP3 ENST00000427242.1 = sample04_batch_1.1.1 1 2 528 sample04 1.0
- - u sample04_batch_1.5.1 4 2 2582 sample04 nan
- - u sample04_batch_1.8.1 2 2 1323 sample04 nan
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
CDC42P1 ENST00000456658.1 k sample05_batch_1.12.1 1 29 1406 sample05 2.0
NCOA5 ENST00000290231.9 i sample05_batch_1.9.1 2 22 357 sample05 2.0
TARDBPP1 ENST00000442013.1 k sample05_batch_1.2.1 2 3 2611 sample05 2.0
NCOA5 ENST00000290231.9 i sample05_batch_1.10.1 2 2 329 sample05 2.0
TPM3P2 ENST00000397772.2 s sample05_batch_1.7.1 3 2 2066 sample05 2.0
TPM3P2 ENST00000397772.2 s sample05_batch_1.7.2 3 2 2067 sample05 2.0
TARDBPP1 ENST00000442013.1 o sample05_batch_1.2.2 4 2 1903 sample05 2.0
CDC42P1 ENST00000456658.1 = sample05_batch_1.13.1 1 0 548 sample05 2.0
FTLP3 ENST00000427242.1 = sample05_batch_1.1.1 1 2 528 sample05 1.0
CFAP61 ENST00000245957.8 x sample05_batch_1.6.1 3 3 852 sample05 1.0
RP5-836E8.1 ENST00000400616.2 x sample05_batch_1.4.1 1 12 1899 sample05 1.0
LINC00851 ENST00000423033.1 x sample05_batch_1.5.1 3 2 2253 sample05 1.0
DDX27 ENST00000622530.3 s sample05_batch_1.11.1 3 2 315 sample05 1.0
PTGIS ENST00000244043.4 i sample05_batch_1.14.1 2 2 677 sample05 1.0
MACROD2 ENST00000217246.7 i sample05_batch_1.15.1 2 2 1713 sample05 1.0
- - u sample05_batch_1.3.1 2 2 713 sample05 nan
- - u sample05_batch_1.8.1 2 2 1323 sample05 nan
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
NCOA5 ENST00000290231.9 i sample06_batch_1.11.1 2 24 357 sample06 2.0
TARDBPP1 ENST00000442013.1 k sample06_batch_1.2.1 2 3 2611 sample06 2.0
NCOA5 ENST00000290231.9 i sample06_batch_1.12.1 2 2 329 sample06 2.0
TARDBPP1 ENST00000442013.1 = sample06_batch_1.2.2 1 0 1203 sample06 2.0
RP5-836E8.1 ENST00000400616.2 x sample06_batch_1.4.1 1 12 1899 sample06 1.0
CDC42P1 ENST00000456658.1 = sample06_batch_1.10.1 1 4 548 sample06 1.0
TPM3P2 ENST00000397772.2 s sample06_batch_1.7.1 3 5 2066 sample06 1.0
RPL21P3 ENST00000395517.2 s sample06_batch_1.5.1 2 2 543 sample06 1.0
DDX27 ENST00000622530.3 s sample06_batch_1.13.1 3 3 315 sample06 1.0
CBFA2T2 ENST00000375279.5 i sample06_batch_1.8.1 2 2 345 sample06 1.0
ADA ENST00000372874.7 x sample06_batch_1.14.1 3 2 634 sample06 1.0
MACROD2 ENST00000217246.7 i sample06_batch_1.15.1 2 2 2058 sample06 1.0
FTLP3 ENST00000427242.1 = sample06_batch_1.1.1 1 1 528 sample06 1.0
- - u sample06_batch_1.3.1 2 2 713 sample06 nan
- - u sample06_batch_1.6.1 4 2 2582 sample06 nan
- - u sample06_batch_1.9.1 2 2 1323 sample06 nan

Differential expression

This section shows differential gene expression and differential isoform usage. Salmon was used to assign reads to individual annotated isoforms defined by the GTF-format annotation. These counts were used to perform a statistical analysis to identify the genes and isoforms that show differences in abundance between the experimental conditions. Any novel genes or transcripts that do not have relevant gene or transcript IDs are prefixed with MSTRG for use in differential expression analysis. Find the full sequences of any transcripts in the final_non_redundant_transcriptome.fasta file.

Alignment summary stats
Statistic sample01 sample02 sample03 sample04 sample05 sample06
Total Read Mappings 3889 3972 3945 3827 3510 3515
Primary 1533 1573 1560 1432 1334 1364
Secondary 2303 2337 2328 2317 2115 2083
Supplementary 53 62 57 78 61 68
Transcripts Per Million

Table showing the annotated Transcripts Per Million identified by Minimap2 mapping and Salmon transcript detection. Displaying the top 100 transcripts with the highest number of mapped reads

Reference sample01 sample02 sample03 sample04 sample05 sample06
MSTRG.75.1 783030 764483 775481 722231 732046 708881
MSTRG.74.3 102566 120125 115970 82692 81741 80560
MSTRG.3.1 19493 25423 16308 9159 14692 13544
ENST00000306750.3 11744 12730 11228 15415 11465 18651
ENST00000621099.1 7284 6909 6964 18253 17568 20244
ENST00000441208.1 7905 6970 7665 13114 10607 12842
ENST00000558175.1 611 580 585 5366 10331 8503
ENST00000620523.1 538 680 686 8542 7140 7480
MSTRG.12.1 0 0 0 9601 5686 6553
ENST00000619753.1 2605 2224 2615 3427 3456 3077
MSTRG.13.1 936 888 895 4545 4233 4878
MSTRG.85.1 0 0 0 5234 5038 5805
ENST00000471144.1 2496 2215 2386 2421 2622 3021
ENST00000433766.1 2006 1522 1918 3520 2903 2974
ENST00000372523.1 1191 822 1243 2850 3527 3161
ENST00000372824.4 3181 3148 3174 519 667 576
MSTRG.54.1 0 0 0 3599 3464 3991
ENST00000620080.1 2110 1334 2017 1762 1696 1954
ENST00000484427.4 1808 1604 1728 1753 1688 2026
MSTRG.55.1 2103 2138 2155 1318 906 1044
MSTRG.55.2 2102 2137 2154 1317 905 1043
ENST00000488495.1 850 806 812 2130 2050 2362
ENST00000623513.1 1352 962 1293 1694 1427 2114
ENST00000412321.1 0 0 0 2239 2515 3726
MSTRG.10.1 827 784 791 2073 1596 1609
ENST00000457423.1 0 0 0 2425 2334 2689
ENST00000456177.4 1072 711 820 1612 1681 1490
ENST00000416600.5 1226 1095 1126 1145 1305 1236
ENST00000606570.1 1037 843 496 1764 1341 1545
ENST00000342374.4 585 431 559 2200 1176 1988
ENST00000428216.3 1166 1061 1069 1103 1291 1190
ENST00000452270.4 937 889 896 1175 1130 1303
ENST00000396825.3 502 416 480 1258 1589 1134
ENST00000543126.1 537 666 672 1036 897 1437
ENST00000361033.1 1124 1279 931 469 632 728
ENST00000482747.1 940 1070 1618 471 453 522
ENST00000487587.2 341 323 326 1709 1028 1185
ENST00000526566.2 249 236 238 1250 1203 1734
ENST00000217109.7 540 384 322 1269 1059 1220
ENST00000476058.4 1183 1283 1616 211 203 234
ENST00000279052.9 525 498 502 1185 1141 876
ENST00000484855.2 282 267 269 1238 1191 1177
ENST00000425473.1 1440 1366 1376 0 0 0
ENST00000190983.4 147 139 140 923 1600 1024
MSTRG.65.1 0 0 0 1274 1226 1413
ENST00000427242.1 0 0 0 1230 1183 1364
ENST00000336095.9 416 359 326 807 959 842
ENST00000244043.4 102 97 97 1347 1235 782
ENST00000465000.1 0 0 0 875 1684 970
ENST00000437016.1 981 931 938 0 591 0
ENST00000305817.2 292 277 209 733 794 1118
ENST00000464883.4 485 460 464 851 468 674
MSTRG.45.1 150 143 144 945 910 1048
ENST00000372865.4 0 0 0 869 1506 964
ENST00000542869.2 203 193 194 892 859 990
ENST00000217185.3 126 120 121 953 918 1057
ENST00000489667.1 119 113 114 1499 577 831
ENST00000608066.4 0 0 0 1045 1006 1159
ENST00000432629.1 1104 1048 1056 0 0 0
ENST00000372868.5 0 0 0 834 1446 925
ENST00000456658.1 0 0 0 976 940 1083
ENST00000400616.2 992 941 948 0 0 0
ENST00000611732.3 1323 836 674 0 0 0
MSTRG.9.1 578 767 663 289 278 160
MSTRG.9.3 577 767 663 289 278 160
MSTRG.9.2 577 766 662 289 278 160
MSTRG.9.4 575 763 660 288 277 159
ENST00000339089.9 312 296 298 587 565 651
ENST00000494921.1 255 242 244 801 616 533
ENST00000493450.1 201 191 192 757 607 700
ENST00000373872.7 1210 738 578 0 0 0
ENST00000244051.2 393 373 376 492 338 546
ENST00000373874.5 1200 732 574 0 0 0
ENST00000439951.5 225 213 215 752 452 625
ENST00000499879.5 323 394 573 520 222 449
ENST00000506387.1 235 223 225 492 758 546
MSTRG.89.1 0 0 0 800 770 888
ENST00000358053.3 222 210 212 742 446 617
MSTRG.23.1 0 0 0 0 1123 1294
ENST00000372806.6 313 382 556 505 216 435
ENST00000409299.6 150 190 192 503 545 767
ENST00000395822.6 0 0 0 750 722 832
ENST00000334534.8 187 356 314 647 339 456
ENST00000262547.8 571 619 780 102 98 113
ENST00000461188.4 110 104 105 553 865 536
ENST00000439981.1 779 739 745 0 0 0
ENST00000616177.3 0 0 0 734 707 814
ENST00000478389.4 409 466 705 205 197 227
ENST00000337227.7 226 215 216 473 546 525
ENST00000313733.6 145 137 138 727 437 605
ENST00000371173.6 0 0 0 703 676 779
ENST00000471629.1 0 0 0 545 787 755
ENST00000467101.4 106 100 101 666 513 591
MSTRG.8.1 462 548 331 289 278 160
ENST00000371610.5 62 59 59 391 678 781
ENST00000613361.1 215 204 205 404 389 598
ENST00000360816.6 114 108 109 500 550 633
ENST00000375279.5 407 491 602 139 134 205
ENST00000373508.1 293 278 280 367 353 407
ENST00000358293.6 111 105 106 488 537 618
Differential gene expression

Table showing the genes from the edgeR analysis. Information shown includes the log2 fold change between experimental conditions, the log-scaled counts per million measure of abundance and the FDR-corrected p-value (False discovery rate - Benjamini-Hochberg). This table has not been filtered for genes that satisfy statistical or magnitudinal thresholds

gene_id gene_name logFC logCPM F PValue FDR
ENSG00000101104.11 PABPC1L -3.3 13.52 861.73 2.04893983490373e-06 0.0001686394657107
ENSG00000124120.9 TTPAL 3.26 12.88 837.03 2.19012293130818e-06 0.0001686394657107
MSTRG.18 None -4.17 14.1 367.39 1.43820986607033e-05 0.0003340023043604
ENSG00000149639.13 SOGA1 -1.99 13.44 358.76 1.51819229254751e-05 0.0003340023043604
MSTRG.55 MSTRG.55 -1.88 14.04 411.9 1.10820151282025e-05 0.0003340023043604
ENSG00000277301.1 RP5-1184F4.7 2.64 13.93 372.17 1.39650572490245e-05 0.0003340023043604
MSTRG.13 MSTRG.13 1.39 13.97 461.8 8.53725384998781e-06 0.0003340023043604
ENSG00000101265.14 RASSF2 -1.62 13.09 995.71 2.97529861555888e-05 0.000572744983495
MSTRG.75 MSTRG.75 -1.03 17.64 138.33 0.0001309699863903 0.0022410419893458
MSTRG.74 MSTRG.74 -1.39 16.25 130.35 0.0001495874161654 0.0023036462089474
ENSG00000126001.14 CEP250 -1.59 12.86 121.21 0.0001810242864593 0.0025343400104311
ENSG00000124256.13 ZBP1 5.79 12.15 754.05 0.0002794578948296 0.0033416107681658
ENSG00000232712.5 KIZ-AS1 6.24 12.47 748.64 0.0002820840258841 0.0033416107681658
ENSG00000101082.12 SLA2 4.81 11.56 780.77 0.0003723465091074 0.0038227574935027
MSTRG.65 MSTRG.65 4.81 11.56 780.77 0.0003723465091074 0.0038227574935027
MSTRG.84 None -0.79 15.41 82.53 0.0004123696394989 0.0039690577801776
MSTRG.9 MSTRG.9 -2.35 13.68 79.68 0.0004454636474708 0.0040353765712062
ENSG00000198326.9 TMEM239 -1.78 13.24 65.52 0.0006830700236383 0.0058440435355723
ENSG00000279253.1 RP4-614O4.13 -4.36 11.15 69233.51 0.0010730458973833 0.0068853778415433
ENSG00000231703.2 RP4-669H2.1 4.69 11.5 295.8 0.0009400617058486 0.0068853778415433
ENSG00000196227.9 FAM217B 1.39 13.11 75.71 0.0010101256878252 0.0068853778415433
ENSG00000149656.7 LINC00266-1 -4.36 11.15 69233.51 0.0010730458973833 0.0068853778415433
ENSG00000198646.12 NCOA6 -4.36 11.15 69233.51 0.0010730458973833 0.0068853778415433
ENSG00000101213.6 PTK6 1.56 12.88 340.3 0.0009705141660462 0.0068853778415433
ENSG00000101158.11 NELFCD -2.22 12.98 49.63 0.0012427980531347 0.0076556360073103
MSTRG.53 None -1.19 15.38 46.42 0.0014333041609254 0.0084895707993275
ENSG00000125827.7 TMX4 -3.25 12.47 44.15 0.0015943629994155 0.0090937741448148
ENSG00000197670.6 RP4-724E16.2 4.42 11.37 793.67 0.0020551999364696 0.0105714669172018
MSTRG.56 MSTRG.56 -2.36 11.73 3266.22 0.0020009986484422 0.0105714669172018
ENSG00000088888.16 MAVS -0.81 16.06 39.09 0.0020593766721821 0.0105714669172018
MSTRG.80 None 4.22 13.66 35.91 0.0024588173027996 0.0122147698268109
MSTRG.88 None 2.53 13.11 34.95 0.0026020532830499 0.0125223814246779
MSTRG.3 MSTRG.3 -1.6 12.62 29.56 0.0036717321524879 0.0171347500449436
ENSG00000089199.8 CHGB 4.25 11.3 84.16 0.0047244062397139 0.0213987812034104
MSTRG.12 MSTRG.12 6.06 12.33 80.84 0.0049722318060015 0.021877819946407
ENSG00000228422.3 LINC00687 2.72 12.5 23.62 0.0057640718736545 0.0246574185706333
ENSG00000124171.7 PARD6B 2.3 12.22 23.13 0.0060066668194171 0.0250007213564929
ENSG00000226308.1 RP4-813D12.3 5.66 12.06 65.9 0.0064411893108837 0.0261037672072656
ENSG00000255438.2 CTD-2653D5.1 1.54 12.44 73.31 0.007069099737893 0.0279138810162956
ENSG00000118707.8 TGIF2 -8.25 13.69 58.6 0.00746951762825 0.0287576428687625
ENSG00000166619.11 BLCAP 4.42 11.37 46.81 0.0098974385246389 0.0371757447023025
MSTRG.86 None 3.86 11.15 806.67 0.0118508561283252 0.0396746052991756
ENSG00000078814.14 MYH7B 3.86 11.15 806.67 0.0118508561283252 0.0396746052991756
ENSG00000179935.8 LINC00652 3.86 11.15 806.67 0.0118508561283252 0.0396746052991756
ENSG00000272874.1 RP5-1103G7.10 3.86 11.15 806.67 0.0118508561283252 0.0396746052991756
ENSG00000130589.15 HELZ2 3.86 11.15 806.67 0.0118508561283252 0.0396746052991756
ENSG00000149646.11 CNBD2 2.03 12.06 15.96 0.0122536276404115 0.0401501841834759
ENSG00000130703.14 OSBPL2 0.79 13.56 25.74 0.0178631197797991 0.0445326955443119
ENSG00000042062.10 FAM65C 4.42 11.37 27.71 0.018889306017642 0.0445326955443119
ENSG00000101181.16 MTG2 1.37 12.33 210.04 0.0200853991529599 0.0445326955443119
ENSG00000132824.12 SERINC3 0.82 13.63 12.11 0.0201872273385665 0.0445326955443119
ENSG00000101247.16 NDUFAF5 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000101350.7 KIF3B -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000125779.20 PANK2 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000131051.19 RBM39 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000182463.14 TSHZ2 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000215388.3 ACTG1P3 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000223891.4 OSER1-AS1 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000261411.1 RP11-268G13.1 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000269202.1 RP4-614O4.12 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000269549.2 RP3-461P17.10 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000277550.1 RP5-1057B20.3 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000280387.1 RP5-1153D9.5 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
MSTRG.11 None -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
MSTRG.14 None -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
MSTRG.2 MSTRG.2 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
MSTRG.48 MSTRG.48 -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
MSTRG.90 None -3.43 10.88 160154.39 0.0207396187804201 0.0445326955443119
ENSG00000206249.3 CTD-2308N23.2 -2.65 11.22 11.9 0.0208204810337043 0.0445326955443119
ENSG00000125875.12 TBC1D20 1.65 12.5 13.99 0.0156028632570054 0.0445326955443119
ENSG00000101144.11 BMP7 4.93 11.62 35.45 0.0139748797495028 0.0445326955443119
ENSG00000280213.1 UCKL1-AS1 -1.96 11.56 2158.8 0.0168099659381147 0.0445326955443119
ENSG00000172296.11 SPTLC3 3.62 11.06 41.72 0.0216022642970656 0.0455719000239466
MSTRG.45 MSTRG.45 1.7 11.88 416.26 0.0259258406680751 0.0539537765254536
ENSG00000244005.11 NFS1 -0.52 14.15 16.97 0.0372139071804746 0.0764125560772411
ENSG00000240849.9 TMEM189 1.6 11.83 268.98 0.038525278933601 0.0780643809970335
ENSG00000184402.13 SS18L1 3.33 10.98 18.05 0.0399023767462215 0.0798047534924431
MSTRG.8 MSTRG.8 -1.25 11.93 9.67 0.052038068594661 0.101441298273137
ENSG00000168612.4 ZSWIM1 0.62 13.78 6.8 0.0517746799096193 0.101441298273137
ENSG00000064601.15 CTSA 1.17 12.22 115.73 0.0538730641071902 0.103705648406341
ENSG00000080839.10 RBL1 1.5 11.78 12.69 0.0568265427515332 0.108040587453532
ENSG00000131044.15 TTLL9 -0.5 14.01 13.6 0.0592645857490931 0.111301782992199
ENSG00000214535.3 RPS15AP1 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000226239.1 RP1-310O13.7 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000256222.2 MTRNR2L3 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000260032.1 LINC00657 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000260257.2 RP5-1085F17.3 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000268628.2 RP1-122P22.4 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
MSTRG.1 None 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
MSTRG.54 MSTRG.54 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
MSTRG.6 None 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
MSTRG.60 MSTRG.60 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
MSTRG.68 None 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
MSTRG.85 MSTRG.85 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
MSTRG.89 MSTRG.89 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000158901.10 WFDC8 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000101079.19 NDRG3 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000124092.11 CTCFL 4.69 11.5 9.61 0.0642257322024461 0.11237859739654
ENSG00000125885.12 MCM8 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000101346.10 POFUT1 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000101266.15 CSNK2A1 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000149488.12 TMC2 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000101190.11 TCFL5 2.96 10.88 815.73 0.0751623086483353 0.11237859739654
ENSG00000232406.5 RP11-234K24.3 -0.23 15.87 31.9 0.0855108015366425 0.125623216676024
ENSG00000101109.10 STK4 -0.66 14.04 4.76 0.0856521931881982 0.125623216676024
ENSG00000197296.5 FITM2 0.59 13.39 4.69 0.0937459380157205 0.136196928815292
ENSG00000101417.10 PXMP4 0.81 12.65 12.73 0.0963536663243104 0.13739319086985
ENSG00000171864.4 PRND 0.81 12.65 12.73 0.0963536663243102 0.13739319086985
ENSG00000101280.7 ANGPT4 -2.91 10.78 5.73 0.109596022583853 0.154842086953334
ENSG00000149609.5 C20orf144 -1.4 11.37 995.31 0.120843605168257 0.16918104723556
ENSG00000101138.10 CSTF1 0.58 13.15 13.35 0.135338999746521 0.187767621269949
ENSG00000124217.4 MOCS3 -0.66 12.68 36.96 0.143248359785051 0.196966494704445
MSTRG.78 MSTRG.78 2.46 10.78 3.66 0.165669225752621 0.218061129543786
ENSG00000101019.20 UQCC1 3.33 10.98 3.66 0.16566981919885 0.218061129543786
ENSG00000232388.4 LINC00493 2.46 10.78 3.66 0.165669225752621 0.218061129543786
ENSG00000225069.3 RP5-1025A1.2 2.46 10.78 3.66 0.165669225752621 0.218061129543786
ENSG00000125843.9 AP5S1 2.46 10.78 3.66 0.165669225752621 0.218061129543786
ENSG00000233048.1 RP5-1069C8.2 2.46 10.78 3.44 0.174623687583209 0.225983595695918
MSTRG.16 MSTRG.16 2.46 10.78 3.44 0.174623687583209 0.225983595695918
ENSG00000101452.13 DHX35 0.86 12.06 283.8 0.179314492259445 0.230120265066288
MSTRG.23 MSTRG.23 2.46 10.78 3.09 0.191011969597271 0.243106143123799
ENSG00000174306.20 ZHX3 -0.76 12.06 11.31 0.201310492158829 0.254113244200489
ENSG00000274825.1 RP4-616B8.5 -0.89 11.68 23.76 0.224652802926813 0.281272615046579
ENSG00000226203.1 RP4-760C5.5 0.99 11.56 10.1 0.244916515711306 0.304170511447913
ENSG00000158445.7 KCNB1 0.67 11.98 28.13 0.307909040749681 0.379343938203606
ENSG00000101236.15 RNF24 0.32 13.56 2.77 0.320293294289671 0.390236115181549
ENSG00000124243.16 BCAS4 -0.67 11.83 26.7 0.321818094987381 0.390236115181549
ENSG00000280240.1 AL049794.1 -0.39 12.83 6.4 0.350325907022204 0.42148585688609
ENSG00000277287.1 RP4-794I6.4 -0.96 11.06 2.1 0.393064340132652 0.469239599848282
MSTRG.27 None -0.42 12.4 6.43 0.406853596887818 0.481965030159416
ENSG00000026559.12 KCNG1 0.46 12.26 2.22 0.41200606998174 0.48434301356632
ENSG00000101448.12 EPPIN 0.65 11.44 2.18 0.47092198548646 0.545278088606528
ENSG00000101294.15 HM13 0.65 11.44 5.65 0.470921985614729 0.545278088606528
ENSG00000125821.10 DTD1 0.46 11.88 5.61 0.502967396877818 0.57803715760585
ENSG00000131061.12 ZNF341 -0.49 11.56 81.79 0.529891521091412 0.600024222412335
ENSG00000204117.1 RP4-640H8.2 -0.49 11.56 81.79 0.529891521091412 0.600024222412335
ENSG00000025293.14 PHF20 -0.26 12.47 17.3 0.605186577194245 0.67868588243158
ENSG00000089050.13 RBBP9 0.3 12.19 3.93 0.608173063477649 0.67868588243158
ENSG00000101276.13 SLC52A3 0.44 11.37 48.83 0.635756667443468 0.684661026477581
ENSG00000125999.9 BPIFB1 0.44 11.37 48.83 0.635756667443468 0.684661026477581
ENSG00000196209.11 SIRPB2 0.44 11.37 48.83 0.635756667443468 0.684661026477581
ENSG00000101003.9 GINS1 0.44 11.37 48.83 0.635756667443468 0.684661026477581
ENSG00000277965.1 Metazoa_SRP 0.44 11.37 48.83 0.635756667443468 0.684661026477581
ENSG00000224008.1 LINC01441 -0.13 13.74 1.17 0.647163161022528 0.690808307257838
MSTRG.10 MSTRG.10 0.21 12.68 3.01 0.650436393197315 0.690808307257838
ENSG00000274414.1 RP5-965G21.4 -0.47 11.15 87.14 0.65690926308277 0.692904291196895
ENSG00000088340.14 FER1L4 0.23 12.26 0.22 0.673206918055159 0.700499090408747
ENSG00000149346.13 SLX4IP -0.18 12.76 0.33 0.672798524953491 0.700499090408747
ENSG00000124209.3 RAB22A -0.23 11.98 5.67 0.717747409493552 0.741832893033604
ENSG00000125991.17 ERGIC3 0.15 12.65 0.61 0.745696359489473 0.765581595742526
ENSG00000277938.1 RP5-965G21.3 0.2 11.78 1.45 0.77441782079674 0.789803605315881
ENSG00000089006.15 SNX5 0.05 13.53 0.03 0.888140058241916 0.899826111639836
ENSG00000020256.18 ZFP64 -0.1 11.22 0.01 0.92090020977422 0.92090020977422
ENSG00000237914.4 SIRPG-AS1 -0.04 13.15 0.04 0.917342310469624 0.92090020977422
Results of the edgeR Analysis.

This plot visualises differences in measurements between the two experimental conditions. M is the log2 ratio of gene expression calculated between the conditions. A is a log2 transformed mean expression value. The figure below presents the MA figure from this edgeR analysis. Genes that satisfy the logFC and FDR-corrected (False discovery rate - Benjamini-Hochberg) p-value thresholds defined are shaded as 'Up-' or 'Down-' regulated.

Differential Isoform usage

Table showing gene isoforms, ranked by adjusted p-value, from the DEXSeq analysis. Information shown includes the log2 fold change between experimental conditions, the log-scaled transcript abundance and the false discovery corrected p-value (FDR - Benjamini-Hochberg) . This table has not been filtered for genes that satisfy statistical or magnitudinal thresholds

gene_id:transcript_id gene_name Log2MeanExon Log2FC pvalue padj
ENSG00000078699.20: ENST00000543126.1 None 4.28980035870982 1.11130882643021 3.86194394573244e-06 0.0001853733093951
ENSG00000078699.20: ENST00000346541.6 None 2.82585108169549 -1.89615754303438 5.51979876191252e-05 0.001324751702859
ENSG00000078699.20: ENST00000375279.5 None 2.94963020587163 -1.38157896646959 0.0010947399012878 0.0175158384206062
ENSG00000101109.10: ENST00000487587.2 None 2.19348358327467 1.74417721295328 0.002305372678466 0.0276644721415923
ENSG00000124120.9: ENST00000461134.1 None 1.20952590536526 -0.659632680966351 0.0050634004697965 0.0426424314771698
ENSG00000064205.9: ENST00000190983.4 None 2.18452594935619 -0.583212941239791 0.0053303039346462 0.0426424314771698
ENSG00000089091.15: ENST00000357236.7 None 1.74392958655133 -11.1790378552733 0.155061960951275 0.70181589922793
ENSG00000078699.20: ENST00000397800.4 None 2.11195118970198 0.804209320985802 0.159921207757099 0.70181589922793
ENSG00000089091.15: ENST00000262547.8 None 1.99445335308279 0.259464272674001 0.174968282670136 0.70181589922793
ENSG00000089091.15: ENST00000476058.4 None 1.99445335308279 0.259464272675802 0.174968282670136 0.70181589922793
ENSG00000124120.9: ENST00000372904.6 None 1.93021916422466 11.624320997497 0.175453974806982 0.70181589922793
ENSG00000124120.9: ENST00000262605.7 None 1.93021916422466 11.6242721347545 0.175453974806982 0.70181589922793
ENSG00000089091.15: ENST00000377630.8 None 1.55699909529106 -10.9946037210427 0.205752572685727 0.712612398422994
ENSG00000101109.10: ENST00000372806.6 None 2.99334186348085 -0.376655223725512 0.222691374507186 0.712612398422994
ENSG00000101109.10: ENST00000499879.5 None 2.99334186348085 -0.37665522403163 0.222691374507186 0.712612398422994
ENSG00000078699.20: ENST00000342704.9 None 2.6678285867525 -0.365648561305133 0.389617616836314 1.0
ENSG00000130703.14: ENST00000313733.6 None 2.25516800072873 0.415382994390735 0.45338411150119 1.0
ENSG00000101213.6: ENST00000542869.2 None 2.39517827603586 -0.307449158068769 0.480298779626055 1.0
ENSG00000101213.6: ENST00000217185.3 None 2.07662125194327 0.469627350381295 0.480389648146724 1.0
ENSG00000078699.20: ENST00000359606.3 None 2.1811424546884 0.366817849031093 0.522215052721103 1.0
ENSG00000064205.9: ENST00000372868.5 None 2.04918574378776 11.9575792811586 0.544189345504777 1.0
ENSG00000064205.9: ENST00000372865.4 None 2.04918574378776 11.9575792811629 0.544189345504777 1.0
ENSG00000078699.20: ENST00000492345.4 None 1.88757377099723 -0.218151008586497 0.691259097106153 1.0
ENSG00000118707.8: ENST00000373874.5 None 2.05386553539864 0.0472910892041503 0.692013183699925 1.0
ENSG00000118707.8: ENST00000373872.7 None 2.05386553539864 0.0473108549132455 0.692013183699925 1.0
ENSG00000064205.9: ENST00000465000.1 None 1.80881116803548 11.7097537421463 0.700161046896988 1.0
ENSG00000101265.14: ENST00000478553.1 None 1.72492572511433 -0.206520438360758 0.708442797442293 1.0
ENSG00000130703.14: ENST00000439951.5 None 2.37321657127766 -0.169574947643042 0.719911506055221 1.0
ENSG00000130703.14: ENST00000358053.3 None 2.37321657127766 -0.169574947643042 0.719911506055221 1.0
ENSG00000118707.8: ENST00000611732.3 None 2.18878730779682 -0.0901999399971567 0.750107946275485 1.0
ENSG00000064205.9: ENST00000471629.1 None 1.68793717857088 11.6165783249147 0.774364942875875 1.0
ENSG00000124228.13: ENST00000484427.4 None 4.79588081506691 -0.0463422440783621 0.838486962048414 1.0
ENSG00000101265.14: ENST00000379376.2 None 1.53534643371677 0.115418389434552 0.847129712161632 1.0
ENSG00000101265.14: ENST00000379400.6 None 1.53534643371677 0.115418389188339 0.847129712161632 1.0
ENSG00000124228.13: ENST00000471144.1 None 4.85299274654391 0.052758850380429 0.849732637414771 1.0
ENSG00000089091.15: ENST00000358866.9 None 0.288243340517197 -9.70538684137039 0.93191315202011 1.0
ENSG00000088888.16: ENST00000428216.3 None 5.48058813301373 0.0121062260718316 0.99019119902513 1.0
ENSG00000088888.16: ENST00000416600.5 None 5.51463456368151 -0.0144120044717431 0.991013488674443 1.0
MSTRG.55: MSTRG.55.2 None 3.25181361959332 -2.1957280438300601e-10 1.0 1.0
MSTRG.55: MSTRG.55.1 None 3.25181361959332 2.19572360293796e-10 1.0 1.0
MSTRG.9: MSTRG.9.2 None 1.81138342915561 -4.83121054273283e-09 1.0 1.0
ENSG00000101158.11: ENST00000478389.4 None 1.97268780435157 2.63011812329239e-09 1.0 1.0
MSTRG.9: MSTRG.9.4 None 1.81138342915561 -4.83121054273283e-09 1.0 1.0
ENSG00000101158.11: ENST00000482747.1 None 1.97268780435157 -2.63011812329239e-09 1.0 1.0
MSTRG.9: MSTRG.9.3 None 1.81138342915561 -4.83121054273283e-09 1.0 1.0
MSTRG.9: MSTRG.9.1 None 1.81138342915561 1.44936311841093e-08 1.0 1.0
ENSG00000196227.9: ENST00000358293.6 None 2.51119697908445 -5.88106896515228e-10 1.0 1.0
ENSG00000196227.9: ENST00000360816.6 None 2.51119697908445 5.88106674470623e-10 1.0 1.0

The figure below presents the MA plot from the DEXSeq analysis. M is the log2 ratio of isoform transcript abundance between conditions. A is the log2 transformed mean abundance value. Transcripts that satisfy the logFC and FDR-corrected (False discovery rate - Benjamini-Hochberg) p-value thresholds defined are shaded as 'Up-' or 'Down-' regulated.

Table showing gene and transcript identifiers and their FDR-corrected (False discovery rate - Benjamini-Hochberg) probabilities for the genes and their isoforms that have been identified as showing DTU using the R packages DEXSeq and StageR. This list has been shortened requiring that both gene and transcript must satisfy the p-value threshold
geneID txID gene transcript gene_name
MSTRG.53 ENST00000342704.9 0.0001853722952059 1.0 CBFA2T2
MSTRG.53 ENST00000397800.4 0.0001853722952059 1.0 CBFA2T2
MSTRG.53 ENST00000492345.4 0.0001853722952059 1.0 CBFA2T2
MSTRG.53 ENST00000359606.3 0.0001853722952059 1.0 CBFA2T2
MSTRG.53 ENST00000346541.6 0.0001853722952059 0.0010349622678586 CBFA2T2
MSTRG.53 ENST00000375279.5 0.0001853722952059 0.0205263731491479 CBFA2T2
MSTRG.53 ENST00000543126.1 0.0001853722952059 7.24114489824833e-05 CBFA2T2
ENSG00000101109.10 ENST00000499879.5 0.0551486344447567 0.835092654401946 STK4
ENSG00000101109.10 ENST00000487587.2 0.0551486344447567 0.0086451475442476 STK4
ENSG00000101109.10 ENST00000372806.6 0.0551486344447567 0.835092654401946 STK4
MSTRG.80 ENST00000372868.5 0.0634830547019462 1.0 WISP2
MSTRG.80 ENST00000190983.4 0.0634830547019462 0.0599659192647701 WISP2
MSTRG.80 ENST00000471629.1 0.0634830547019462 1.0 WISP2
MSTRG.80 ENST00000372865.4 0.0634830547019462 1.0 WISP2
MSTRG.80 ENST00000465000.1 0.0634830547019462 1.0 WISP2
ENSG00000124120.9 ENST00000262605.7 0.0804360383114311 0.657952405526184 TTPAL
ENSG00000124120.9 ENST00000372904.6 0.0804360383114311 0.657952405526184 TTPAL
ENSG00000124120.9 ENST00000461134.1 0.0804360383114311 0.0189877517617372 TTPAL
MSTRG.84 ENST00000471144.1 1.0 nan DDX27
MSTRG.18 ENST00000262547.8 1.0 nan DZANK1
MSTRG.18 ENST00000377630.8 1.0 nan DZANK1
MSTRG.18 ENST00000476058.4 1.0 nan DZANK1
MSTRG.18 ENST00000357236.7 1.0 nan DZANK1
MSTRG.18 ENST00000358866.9 1.0 nan DZANK1
MSTRG.55 MSTRG.55.1 1.0 nan MSTRG.55
ENSG00000088888.16 ENST00000428216.3 1.0 nan MAVS
MSTRG.55 MSTRG.55.2 1.0 nan MSTRG.55
ENSG00000118707.8 ENST00000611732.3 1.0 nan TGIF2
MSTRG.84 ENST00000484427.4 1.0 nan DDX27
ENSG00000118707.8 ENST00000373872.7 1.0 nan TGIF2
ENSG00000118707.8 ENST00000373874.5 1.0 nan TGIF2
ENSG00000088888.16 ENST00000416600.5 1.0 nan MAVS
ENSG00000101158.11 ENST00000482747.1 1.0 nan NELFCD
MSTRG.9 MSTRG.9.4 1.0 nan MSTRG.9
MSTRG.9 MSTRG.9.1 1.0 nan MSTRG.9
MSTRG.9 MSTRG.9.3 1.0 nan MSTRG.9
MSTRG.9 MSTRG.9.2 1.0 nan MSTRG.9
ENSG00000101265.14 ENST00000379376.2 1.0 nan RASSF2
ENSG00000101265.14 ENST00000379400.6 1.0 nan RASSF2
ENSG00000101265.14 ENST00000478553.1 1.0 nan RASSF2
ENSG00000196227.9 ENST00000358293.6 1.0 nan FAM217B
ENSG00000196227.9 ENST00000360816.6 1.0 nan FAM217B
ENSG00000101213.6 ENST00000217185.3 1.0 nan PTK6
ENSG00000101213.6 ENST00000542869.2 1.0 nan PTK6
ENSG00000130703.14 ENST00000313733.6 1.0 nan OSBPL2
ENSG00000130703.14 ENST00000439951.5 1.0 nan OSBPL2
ENSG00000130703.14 ENST00000358053.3 1.0 nan OSBPL2
ENSG00000101158.11 ENST00000478389.4 1.0 nan NELFCD
View dtu_plots.pdf file to see plots of differential isoform usage

Software versions

Name Version
pysam 0.21.0
pandas 1.3.5
scikit-learn 1.0.2
fastcat 0.10.2
minimap2 2.24-r1122
samtools 1.17
bedtools v2.30.0
pychopper 2.7.10
gffread 0.12.7
seqkit v2.2.0
stringtie 2.1.1

Workflow parameters

Key Value
fastq wf-transcriptomes/data/differential_expression/differential_expression_fastq
bam None
ref_genome wf-transcriptomes/data/differential_expression/hg38_chr20.fa
ref_annotation wf-transcriptomes/data/differential_expression/gencode.v22.annotation.chr20.gtf
transcriptome_source reference-guided
threads 4
isoform_table_nrows 5000
out_dir wf-transcriptomes
sample None
sample_sheet wf-transcriptomes/data/differential_expression/sample_sheet.csv
analyse_unclassified False
igv False
direct_rna True
pychopper_opts None
pychopper_backend edlib
cdna_kit SQK-PCS109
minimap2_index_opts -k 15
minimap2_opts -uf
minimum_mapping_quality 40
poly_context 24
max_poly_run 8
bundle_min_reads 50000
stringtie_opts --conservative
gffcompare_opts -R
plot_gffcmp_stats True
store_dir wf-transcriptomes/store_dir
de_analysis True
ref_transcriptome None
min_samps_gene_expr 3
min_samps_feature_expr 1
min_gene_expr 10
min_feature_expr 3