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Old 05-09-2019, 04:54 PM   #1
chayan
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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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Old 05-10-2019, 03:24 AM   #2
GenoMax
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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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bash, bioinformactics, bowtie alignment stats, htseq, htseq count

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