Dear All,
I am using htseq count to get exonic read count fro targeted seq data..
I have output BAM file with alignments and I need to get the read counts for the respective exonics..the exon gtf file looks like this,
chr9 bed2gff exon 133589697 133589852 0 + . ABL1
chr9 bed2gff exon 133709410 133709441 0 + . ABL1
chr9 bed2gff exon 133710251 133710279 0 + . ABL1
And the error I receive from HT SEQ-count is,
Error occurred when processing GFF file (line 1 of file Regions_new.GTF):
Failure parsing GFF attribute line
[Exception type: Value Error, raised in init.py:164]
Pleas elet me know why I am having this error, and the command line I used is,
htseq-count -a 10 -m intersection-strict -s yes mydata.sam Regions_new.GTF
