bash script to find the results from multiple input files which are using 'samtools' to a new output csv file
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I have query related to Bioinformatics. I have multiple bam files, from each bam file i should find out number of mapped reads from each bam file with id's, for doing it i have the command
$ samtools view -c -f 1 -F 12 HG00173.chrom11.ILLUMINA.bwa.FIN.low_coverage.20111114.bam
for this i am getting output in some numbers as 1222456.
My requirement is, I should get the output for all the input bam files in a csv file with 2 columns with naming column 1) Bam-id , column 2) No_of_mapped_reads.
Asked by dexter_danny
(23 rep)
Oct 16, 2019, 11:48 AM
Last activity: Oct 16, 2019, 04:52 PM
Last activity: Oct 16, 2019, 04:52 PM