bash loop to count multiple words from multiple corresponding files

chayan · 05-09-2019, 05:54 PM

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.

GenoMax · 05-10-2019, 04:24 AM

You should consider using featureCounts. You may not need a loop. You can feed all SAM files to featureCounts and generate a read count matrix directly.

Code:

featureCounts <options> file1.sam file2.sam file3.sam etc.

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05-09-2019, 05:54 PM	#1
chayan Member Location: USA Join Date: Nov 2012 Posts: 51	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.

05-10-2019, 04:24 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	You should consider using featureCounts. You may not need a loop. You can feed all SAM files to featureCounts and generate a read count matrix directly. Code: featureCounts <options> file1.sam file2.sam file3.sam etc.