The University Wiki Service has upgraded the Confluence Server software, from version 5.9.14 to 5.10.8. Please refer to the knowledge base article, KB0015891, for a high level summary of upgrade changes. Thank you!
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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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