TrinityStats error cannot decipher gene identifier from acc

[Laura Entrambasaguas]

Hi everybody,

I'm trying to run TrinityStats.pl on a transcriptome, performed by Trinity, that has the following type of contig identifier:

>contig_00001

>contig_00002
.....

Unfortunately, the authors told me that the only way to back to the original ID (output of Trinity) is by Blasting the "problem" contigs with the original ones.

How could I solve this to avoid blasting??

Any help would be highly appreciated.

Thanks so much.

[Mark Chapman]

Hi Laura, Unless your contigs are in the same order in that file as they were in the original trinity file I would presume blasting is the only thing you can do. But the suggestion by your colleagues implies that the original ones are available, so cant you just use those? Or have you done some analysis with the newly names ones?

Best wishes, Mark

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Dr. Mark A. Chapman

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+44 (0)2380 594396

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[Brian Haas]

Hi all,

Here's a drop-in replacement that will be more flexible about what transcript fasta file you use it on.  If it doesn't recognize the Trinity accession, it'll still report based on the transcripts w/o providing gene-level longest isoform info. In other words, it'll still be somewhat useful.   ;-)

best,

~brian