SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
IDBA-UD paired end data on multiple files thh32 Bioinformatics 4 02-27-2014 03:09 AM
bowtie2 multiple single and paired-end files NatashaPavlovikj Bioinformatics 7 07-15-2013 12:55 AM
bowtie2: aligning multiple input files ksw9 Genomic Resequencing 2 05-13-2013 01:59 PM
Aligning paired end read files that have different numbers of reads after trimming d1antho RNA Sequencing 2 01-21-2013 09:41 AM
Aligning paired end Illumina data with Bowtie kopardev Bioinformatics 5 03-29-2012 08:46 AM

Reply
 
Thread Tools
Old 03-17-2016, 12:07 PM   #1
cnash2
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.......
cnash2 is offline   Reply With Quote
Old 03-21-2016, 02:58 PM   #2
shi
Wei Shi
 
Location: Australia

Join Date: Feb 2010
Posts: 235
Default

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

http://bioconductor.org/packages/rel.../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.
shi is offline   Reply With Quote
Reply

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 02:00 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO