XLOC as gene ID?

[JQL]

I saw this old thread and thought would like to bring this alive again.

I am having similar issues. The GTF file I used was from Ensembl where gene IDs are Ensembl IDs. The cuffdiff output file replaced the Ensembl IDs with XLOC_'s although it also output gene names (e.g. BCL2). Ensembl IDs were no longer there.

Is there anyway to convert XLOC back to Ensemble IDs, or simply keep the ensembl IDs from my GTF file? how do you guys go about this? I try to think what was the authors' intention to replace useful IDs with XLOC's?

Interesting enough, if I don't run new gene discovery (i.e. without doing cuffmerge step), I got to keep Ensembl IDs.

thoughts?

http://seqanswers.com/forums/showthread.php?p=87813#post87813

[super0925]

I have same question . I want the Ensembl ID from Cufflinks output however I only get the XLOC ID.
The only way I could do is go back to GTF file and parse the Ensembl ID. But it costs time. Any one has a quicker/smarter idea?

I saw this old thread and thought would like to bring this alive again.

I am having similar issues. The GTF file I used was from Ensembl where gene IDs are Ensembl IDs. The cuffdiff output file replaced the Ensembl IDs with XLOC_'s although it also output gene names (e.g. BCL2). Ensembl IDs were no longer there.

Is there anyway to convert XLOC back to Ensemble IDs, or simply keep the ensembl IDs from my GTF file? how do you guys go about this? I try to think what was the authors' intention to replace useful IDs with XLOC's?

Interesting enough, if I don't run new gene discovery (i.e. without doing cuffmerge step), I got to keep Ensembl IDs.

thoughts?

http://seqanswers.com/forums/showthr...7813#post87813