Entering edit mode
8.4 years ago
hadaarjan
▴
20
How do I know if an alignment is spliced by looking at SAM format? I need to find spliced alignments from BAM file.
How do I know if an alignment is spliced by looking at SAM format? I need to find spliced alignments from BAM file.
search for 'N' in the cigar string?
samtools view in.bam | awk '($6 ~ /N/)'
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.