htseq gtf problem

Question

[kti.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

[GenoMax]

Can you add the htseq-count command you are using? That python error may mean that you are not providing right options.

Does your annotation file contain tab separated fields?

Answer 1

[kti.adler]

indeed there were spaces all over the file... Thank you @genomax