Question: Spliced alignment information from bam file
2
gravatar for hadaarjan
4.7 years ago by
hadaarjan20
United States
hadaarjan20 wrote:

How do I know if an alignment is spliced by looking at SAM format? I need to find spliced alignments from BAM file.

sam bam • 3.3k views
ADD COMMENTlink modified 4.7 years ago by Pierre Lindenbaum129k • written 4.7 years ago by hadaarjan20
2
gravatar for Pierre Lindenbaum
4.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

search for 'N' in the cigar string?

samtools view  in.bam | awk '($6 ~ /N/)'
ADD COMMENTlink modified 7 months ago by RamRS27k • written 4.7 years ago by Pierre Lindenbaum129k
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