Samtools tricks
- Daechan Park
Owned by Daechan Park
Count mapped reads
samtools view -F 0X04 <bam>
Print uniquely mapped reads
samtools view -bq 1 <bam>
Print reversely mapped reads
samtools view -f 0X10 <bam>
Print reversely mapped reads in certain range
samtools view -f 0X10 <bam> chrI:XXX-XXX
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