Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
DESeq2 error in data.frame (multiple treatments and multiple replicates) KYR Bioinformatics 3 03-19-2019 10:05 AM
For loop in bash terminal to concatenate fastq files rcook34 Bioinformatics 6 02-04-2016 08:41 PM
A great tool to count multiple aligned reads. a.kmg Bioinformatics 3 02-22-2015 06:05 AM
htseq-count: how to use multiple features? nasobema Bioinformatics 3 09-15-2014 03:37 AM
how to use bash script to make iterative loop through directory with two file types jddavis Bioinformatics 2 05-23-2013 08:02 AM

Thread Tools
Old 05-09-2019, 05:54 PM   #1
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.
chayan is offline   Reply With Quote
Old 05-10-2019, 04:24 AM   #2
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.

featureCounts <options> file1.sam file2.sam file3.sam etc.
GenoMax is offline   Reply With Quote

bash, bioinformactics, bowtie alignment stats, htseq, htseq count

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:59 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO