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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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rsem-prepare-reference #84

Closed fcamus closed 6 years ago

fcamus commented 6 years ago

Hi there,

I am trying to build a reference with the D.melanogaster genome. I downloaded the fasta and .gtf files from the latest release in flybase (ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.19_FB2017_06/) and got this error:

The GTF file might be corrupted! Stop at line : 3R FlyBase mRNA 21360390 21377399 . gene_id "FBgn0002781"; gene_symbol "mod(mdg4)"; transcript_id "FBtr0084079"; transcript_symbol "mod(mdg4)-RT"; Error Message: Strand is neither '+' nor '-'!

bli25wisc commented 6 years ago

Hi @fcamus, this suggests that your GTF file is corrupted. There should be a strand information (either '+' or '-') between '.' and 'gene_id'.

Hope it helps, Bo