Hard clip reads that overhang the reference sequence in SAM file
Hello
I have aligned some reads using CLC to a reference genome. When I export the reads in SAM format if a read overhangs the reference sequence CLC reports this as a soft clip.
Take for example this (partial) SAM record:
502_1735_1931_F3 16 scaffold_10212 558 0 36S39M [etc.]
CLC aligned only 39 bases of this read to the end of this short contig (596 bases), the rest of 36 nt of the read are hanging beyond the contig boundary and are thus reported soft clipped (which makes sense).
Sadly (as reported in this thread http://seqanswers.com/forums/showthr...9180#post99180) this means that cufflinks will throw an error.
Is there a way to convert the soft trimming into a hard trim?
I have aligned some reads using CLC to a reference genome. When I export the reads in SAM format if a read overhangs the reference sequence CLC reports this as a soft clip.
Take for example this (partial) SAM record:
502_1735_1931_F3 16 scaffold_10212 558 0 36S39M [etc.]
CLC aligned only 39 bases of this read to the end of this short contig (596 bases), the rest of 36 nt of the read are hanging beyond the contig boundary and are thus reported soft clipped (which makes sense).
Sadly (as reported in this thread http://seqanswers.com/forums/showthr...9180#post99180) this means that cufflinks will throw an error.
Is there a way to convert the soft trimming into a hard trim?