Aligning multiple paired-end files with subread

[cnash2]

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.......

[shi]

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

http://bioconductor.org/packages/release/bioc/html/Rsubread.html

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.