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Comment: Migrated to Confluence 5.3
Code Block
titleCount mapped reads
samtools view -F 0X04 <bam>
Code Block
titlePrint uniquely mapped reads
samtools view -bq 1 <bam>
Code Block
titlePrint reversely mapped reads
samtools view -f 0X10  <bam>
Code Block
titlePrint reversely mapped reads in certain range
samtools view -f 0X10  <bam> chrI:XXX-XXX