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Old 03-17-2016, 01:07 PM   #1
Junior Member
Location: Montreal

Join Date: Dec 2015
Posts: 7
Default Aligning multiple paired-end files with subread

Hi all,

Is there anyone out there who knows whether it's possible to align multiple paired-end sequencing fastq files with subread at the same time? For example, we have paired-end sequencing data for 148 samples which we want aligning with subread. We would like to avoid having to set this running sample by sample one at a time. Is there a way to run it in batch for all these samples contained in the same directory? R or command line version solutions would be appreciated, we could use either.......
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Old 03-21-2016, 03:58 PM   #2
Wei Shi
Location: Australia

Join Date: Feb 2010
Posts: 235

The align() function in Bioconductor package Rsubread allows you to provide multiple input files for alignment at the same time:

The align() function is an R wrapper function for the 'subread-align' command in SourceForge Subread package. If you run 'subjunc' command, you can use the subjunc() function in Rsubread as well.
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