Question: Trouble Linking Gene_Ids From *Gtf File To Assembled Transcripts In Cufflinks
gravatar for User 4409
8.5 years ago by
User 440910
User 440910 wrote:

I am having trouble getting Cufflinks to report my transcripts using the accession numbers provided by my *.gtf file. The 9th column of my *gtf file looks like this: geneid "ACYPI006883"; transcriptid "ACYPI006883"; gene_name "ACYPI006883"; so I believe that the *gtf file is properly formatted.

I have run with both the -g and -G options. When I run the -G option, it lists the transcripts with the gene ids and all the FPKM = 0. Nothing else is reported. When I run the -g option, it lists the named genes as FPKM = 0 (as with the -G option) and all the CUFF_ID genes have FPKM numbers. It's almost as if Cufflinks is telling me that it cannot match any of the assembled transcripts to my *gtf file.

I have also tried running Cuffcompare using the -r option, thinking that it might be able to link up the accession numbers, but it doesn't.

Any suggestions?

cufflinks • 2.2k views
ADD COMMENTlink modified 8.4 years ago by Aswarren60 • written 8.5 years ago by User 440910
gravatar for Aswarren
8.5 years ago by
Blacksburg, VA
Aswarren60 wrote:

This has happened to me when the replicon/ contig IDs from the GTF do not match the FASTA header IDs from the indexed genome. Have you checked that?

ADD COMMENTlink written 8.5 years ago by Aswarren60

My fasta genome scaffold names are not the same as the first column of my gtf file. Should these be exactly* the same?

ADD REPLYlink written 8.5 years ago by User 440910

In my experience yes. I believe an exact string match is how cufflinks figures out which annotations belong to which scaffold/replicon.

ADD REPLYlink modified 8.2 years ago • written 8.2 years ago by Aswarren60
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