View Single Post
Old 05-14-2014, 01:14 PM   #30
AddDNAse
Junior Member
 
Location: Wisconsin

Join Date: May 2014
Posts: 3
Default Similar Problem

Hi everyone,

I hope someone is still checking this thread. I am having a very similar problem. I have tried all of the troubleshoots posted here. I keep getting the following:
tracking_id gene_short_name
1 XLOC_000010 <NA>
2 XLOC_000011 <NA>
3 XLOC_000013 <NA>
4 XLOC_000014 <NA>
5 XLOC_000018 <NA>
6 XLOC_000022 <NA>
Where all my gene_short_names are NA with the exception of a handful. When I check the file "genes.fpkm_tracking" in my cuffdiff output folder I have the following:

LOC_000010 - - XLOC_000010 GDH3 TSS15 I:31567-32941 - - 6.88081 0 17.4366 OK 0 0 0 OK 59.5503 32.1558 86.9447 OK 16.1091 0 39.818 OK 12.1495 0 33.8913 OK 8.74331 0 26.3261 OK
XLOC_000011 - - XLOC_000011 BDH2 TSS16 I:33448-34702 - - 7.16722 0 18.5636 OK 1318.72 1267.41 1370.04 OK 525.033 470.782 579.285 OK 16.9807 0 37.6977 OK 10.7936 0 26.9461 OK 7.9163 0 20.9762 OK
XLOC_000012 - - XLOC_000012 BDH1 TSS17 I:35155-36304 - - 8.65006 0 22.6596 OK 456.226 434.267 478.185 OK 812.57 739.725 885.414 OK 20.4021 0 49.5953 OK 16.3412 0 52.9038 OK 15.2207 0 37.045 OK
XLOC_000013 - - XLOC_000013 ECM1 TSS18 I:36496-37148 - - 302.668 243.291 362.045 OK 0 0 0 OK 127.871 38.9611 216.78 OK 9.66232 0 27.5273 OK 4.65527 0 14.9566 OK 5.77583 0 18.0408 OK

Where clearly the XLOC_** numbers are being linked with a gene_short_name. Furthermore, in my merged.gtf file I have the following:

I Cufflinks exon 31568 32941 . + . gene_id "XLOC_000010"; transcript_id "TCONS_00000015"; exon_number "1"; gene_name "GDH3"; oId "YAL062W"; nearest_ref "YAL062W"; class_code "="; tss_id "TSS15"; p_id "P11";
I Cufflinks exon 33449 34702 . + . gene_id "XLOC_000011"; transcript_id "TCONS_00000016"; exon_number "1"; gene_name "BDH2"; oId "YAL061W"; nearest_ref "YAL061W"; class_code "="; tss_id "TSS16"; p_id "P12";
I Cufflinks exon 35156 36304 . + . gene_id "XLOC_000012"; transcript_id "TCONS_00000017"; exon_number "1"; gene_name "BDH1"; oId "YAL060W"; nearest_ref "YAL060W"; class_code "="; tss_id "TSS17"; p_id "P13";
I Cufflinks exon 36510 37148 . + . gene_id "XLOC_000013"; transcript_id "TCONS_00000018"; exon_number "1"; gene_name "ECM1"; oId "YAL059W"; nearest_ref "YAL059W"; class_code "="; tss_id "TSS18"; p_id "P14";

I have upgraded my cummeRbund so that is most likely not the issue. Any suggestions are greatly appreciated!
AddDNAse is offline   Reply With Quote