Hi,
I'm looking for some workflow to obtain the reads which are mapped to the antisense features (gff) of a reference.
I started using HTseq_count (which is a great tool), that takes my sam and gff files, and with the obtion -s no/yes I do obtain (no stranded minus stranded) the the number of antisense reads; but I need the reads themselves (sam or fasta). So, is there a way from a sam file (output from HTseq - no stranded reads) to take off a subset of reads (stranded sam output) and get the final sam file with the antisense pool? Maybe there are better ways to do this.
Thanks
I'm looking for some workflow to obtain the reads which are mapped to the antisense features (gff) of a reference.
I started using HTseq_count (which is a great tool), that takes my sam and gff files, and with the obtion -s no/yes I do obtain (no stranded minus stranded) the the number of antisense reads; but I need the reads themselves (sam or fasta). So, is there a way from a sam file (output from HTseq - no stranded reads) to take off a subset of reads (stranded sam output) and get the final sam file with the antisense pool? Maybe there are better ways to do this.
Thanks
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