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katwre/count_total_number_of_reads.R

Last active August 27, 2015 12:22
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count total number of reads
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count_total_number_of_reads.R
bampath = "example.bam"
command=paste0("samtools idxstats ", bampath," | awk 'BEGIN {a=0} {a += $3 } END{print a }'")
tot.mapped=as.numeric(try(system(command,intern=TRUE)))
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