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Old 05-09-2019, 04:54 PM   #1
chayan
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Location: USA

Join Date: Nov 2012
Posts: 51
Default bash loop to count multiple words from multiple corresponding files

I have generated multiple read mapping files (.sam) generated with bowtie2 "--no-unal" parameter. As the number of files are huge (7 reference genomes mapped against >6000 reads) i want a loop to count the % (or total number) mapped reads for each file.

HTSeq could be an option but don't know how to loop it for multiple files.
Any help would be much appreciated.
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