RSEM build for C. elegans

Question

[Michele Busby]

Hi,

Has anyone had luck getting an RSEM build for worm?

I am using:

rsem-prepare-reference --gtf /Worm/c_elegans.PRJNA13758.WS253.canonical_geneset.gtf \
  --polyA-length 25 --polyA /Worm/c_elegans.PRJNA13758.WS253.genomic_softmasked.fa \
  /Worm/c_elegans.PRJNA13758.WS253/RSEM/transcriptome

And I get:

The GTF file might be corrupted!
Stop at line : I    WormBase    exon    3747    3909    .   -   .   gene_id "WBGene00023193" ; transcript_id "Y74C9A.6"
Error Message: Cannot find transcript_id!

I see the transcript_id in there so I'm not sure what the problem is. I tried using the gff3 and that failed as well. Any thoughts?

Thank you!

Answer 1

[Michele Busby]

I figured it out but I'll leave it here if anyone else runs into this:

RSEM expects a ; after the transcript_id. It's not here in this version of the file.

This adds the : to the line and seems to fix it:

sed -i 's/$/;/' c_elegans.PRJNA13758.WS253.canonical_geneset.fixed.gtf