View Single Post
Old 05-18-2016, 02:12 AM   #1
Location: Sweden

Join Date: May 2014
Posts: 19
Default Can I use htseq --samout file for subsequent annotation?

So briefly what I'm doing is that:
-->I'm annotating my smallRNA sequencing data using htseq-count.
-->I'm using original.sam to annotate miRNAs and using -o to get the out.sam
-->From that out.sam I can grep out the 'no_feature' reads/rows.

The question:
Maybe a stupid idea but is there any way I could use this out_no_feature.sam file for another round of htseq annotationagainst e.g. rRNA.gtf?

As the out_no_feature.sam does not have a header, is there any way to reheader it or use the header from the original.sam file? Also, I guess I need to remove the last column "XF:Z:__no_feature" from the out_no_feature.sam

Thanks ahead for comments and help
heso is offline   Reply With Quote