Discrepancies between --GTF and GTF-guide runs: Isoform results disappearing with GTF-guide

[mpschr]

Hi

I have run cufflinks on the same bamfile, twice with an important difference:

• once with the --GTF option, a normal run (below cufflinks folder),
• and once with the --GTF-guide, a novel-transcript detection run (below: cufflinks_noguide folder)

$ grep -P "TP53\t"  */isoform*
cufflinks/isoforms.fpkm_tracking:ENST00000413465    -   -   CUFF.30922  TP53    -   17:7565096-7579912  1018    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000359597    -   -   CUFF.30922  TP53    -   17:7569403-7579912  1152    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000504937    -   -   CUFF.30922  TP53    -   17:7571719-7578811  2271    83.4765 13.1751 13.1751 13.1751 OK
cufflinks/isoforms.fpkm_tracking:ENST00000504290    -   -   CUFF.30922  TP53    -   17:7571719-7578811  2331    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000510385    -   -   CUFF.30922  TP53    -   17:7571719-7578811  2404    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000269305    -   -   CUFF.30922  TP53    -   17:7571719-7590856  2579    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000420246    -   -   CUFF.30922  TP53    -   17:7571721-7590799  2653    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000455263    -   -   CUFF.30922  TP53    -   17:7571721-7590799  2580    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000445888    -   -   CUFF.30922  TP53    -   17:7571738-7590805  2506    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000576024    -   -   CUFF.30922  TP53    -   17:7572886-7576905  175 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000509690    -   -   CUFF.30922  TP53    -   17:7576852-7590805  729 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000514944    -   -   CUFF.30922  TP53    -   17:7577534-7590745  546 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000574684    -   -   CUFF.30922  TP53    -   17:7577571-7578437  104 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000505014    -   -   CUFF.30922  TP53    -   17:7577843-7590805  1261    0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000508793    -   -   CUFF.30922  TP53    -   17:7578433-7580752  634 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000604348    -   -   CUFF.30922  TP53    -   17:7578479-7590805  568 0   0   0   0   OK
cufflinks/isoforms.fpkm_tracking:ENST00000503591    -   -   CUFF.30922  TP53    -   17:7578546-7590745  565 0   0   0   0   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000413465    -   -   ENSG00000141510 TP53    -   17:7565096-7579912  1018    0   0   0   0.0784283   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000359597    -   -   ENSG00000141510 TP53    -   17:7569403-7579912  1152    0   0   0   0.0710096   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000504937    -   -   ENSG00000141510 TP53    -   17:7571719-7578811  2271    57.4473 9.06728 8.17987 9.95469 OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000504290    -   -   ENSG00000141510 TP53    -   17:7571719-7578811  2331    8.29612e-12 1.30943e-12 0   0.0285236   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000510385    -   -   ENSG00000141510 TP53    -   17:7571719-7578811  2404    2.06479 0.325899    0.140638    0.511161    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000269305    -   -   ENSG00000141510 TP53    -   17:7571719-7590856  2579    6.32227 0.997886    0.692799    1.30297 OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000455263    -   -   ENSG00000141510 TP53    -   17:7571721-7590799  2580    4.16124e-14 6.56796e-15 0   0.0260571   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000420246    -   -   ENSG00000141510 TP53    -   17:7571721-7590799  2653    0.00293471  0.000463204 0   0.0255082   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000445888    -   -   ENSG00000141510 TP53    -   17:7571738-7590805  2506    4.00765 0.632554    0.384194    0.880913    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000576024    -   -   ENSG00000141510 TP53    -   17:7572886-7576905  175 0   0   0   0.363874    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000509690    -   -   ENSG00000141510 TP53    -   17:7576852-7590805  729 0   0   0   0.127829    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000514944    -   -   ENSG00000141510 TP53    -   17:7577534-7590745  546 0   0   0   0.187486    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000574684    -   -   ENSG00000141510 TP53    -   17:7577571-7578437  104 0   0   0   0.612288    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000505014    -   -   ENSG00000141510 TP53    -   17:7577843-7590805  1261    0   0   0   0.0624882   OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000508793    -   -   ENSG00000141510 TP53    -   17:7578433-7580752  634 2.78604e-89 4.39738e-90 0   0.153351    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000604348    -   -   ENSG00000141510 TP53    -   17:7578479-7590805  568 0   0   0   0.166118    OK
cufflinks_noguide/isoforms.fpkm_tracking:ENST00000503591    -   -   ENSG00000141510 TP53    -   17:7578546-7590745  565 0   0   0   0.167144    OK

When I look at a known transcript in the GTF-guide run, I observe that many isoforms are missing that were reported with an FPKM value when with the normal run.

I'd think there is something wrong with one of the results - or is there an explanation for it?