The getNumReads script reads all files in the working directory with regular expression *.bam, and for each bam file, prints the file name, the count for all reads in the file, and the count for all mapped reads in the file. getNumReads uses the script samtools. More information on samtools can be found here.
getNumReads is called with the following command line prompt:
Running getNumReads with the following command line prompt:
In a directory that contains the following files:
Will produce the following results in the command line:
Bp0071_2_S90-bowtie2 203096 170848
Bp7709_S66-bowtie2 112288 2099
Bp8815_S143-bowtie2 168658 39010