#35 htseq count problem

[katy adler]

Hello
i am having a problem runnig the htseq quantification on a bam built using STAR 2.6.0a and a GTF file

i am trying to quantify the bam using the same GTF file as for genome indexes,
but it fails, giving me this ERROR

Error occured when processing GFF file (line 1 of file my.gtf):
need more than 1 value to unpack

the gtf looks like this:

NC_001348.1 RefSeq CDS 173 562 . + 0 transcript_id "gene0"; gene_id "gene0"; gene_name "ORF0";
NC_001348.1 RefSeq CDS 589 915 . - 0 transcript_id "gene1"; gene_id "gene1"; gene_name "ORF1";
NC_001348.1 RefSeq CDS 1185 1850 . + 0 transcript_id "gene2"; gene_id "gene2"; gene_name "ORF2";
NC_001348.1 RefSeq CDS 1908 2447 . - 0 transcript_id "gene3"; gene_id "gene3"; gene_name "ORF3";

what could be probably my problem?

thanks,
katy

[Simon Anders]

Hi Katy

the SourceForge page is dead since years. Please repost your support request on GitHub:

https://github.com/simon-anders/htseq/issues

Simon