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Old 05-11-2010, 12:29 PM   #1
RockChalkJayhawk
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Default Cufflinks no p_ID but has TSS_ID

I just finished running multiple samples using cufflinks and cuff diff. I used a Hg19.GTF file that has CDS information, but when I run cuffdiff, my cds.fpkm_tracking file is empty.

Has anyone else had this problem? How do I fix it?
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Old 05-12-2010, 01:48 AM   #2
dariober
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Hi,
Asked roughly an equivalent question days ago. Check this post 05-06-2010 "cufflinks / cuffcompare does not produce p_id". See if it helps a bit...
If you manage to fix it, I'd like to know how.

All the best
Dario
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Old 05-12-2010, 04:47 AM   #3
RockChalkJayhawk
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It sounds like we need to wait for a new release...however, at least the isoform analysis is done and you can manually look to see if there is a different CDS...
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Old 07-14-2010, 09:44 PM   #4
jetspeeder
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I am still getting the same issue with the 0.8.3 version, I see the tss_id in my combined.gtf file, but I do not see a p_id even though the reference file I provided, UCSC KnownGenes GTF has the CDS information. Anyone else experiencing similar problems? Thanks.
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Old 12-08-2010, 06:33 AM   #5
jgoecks
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Bump. I'll still seeing this problem in version 0.9.1 Any ideas or fixes?

Thanks,
J.
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Old 12-08-2010, 06:36 AM   #6
fkuo
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did you use this option when you ran cuffcompare?


-s <seq_dir> Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.

I think you need to use that to the P_id show up.
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Old 12-08-2010, 07:33 AM   #7
jgoecks
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Yes, that worked. Thanks!
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