SEQanswers (
-   Bioinformatics (
-   -   Aligning multiple paired-end files with subread (

cnash2 03-17-2016 12:07 PM

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.......

shi 03-21-2016 02:58 PM

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.

All times are GMT -8. The time now is 03:28 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.