SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
processing pindel output files odoyle81 Bioinformatics 9 01-17-2017 10:10 PM
How to batch download thousands of FASTA files? J:Mo Bioinformatics 6 12-18-2014 02:00 PM
ab1 files batch printing thedamian Sanger/Dye Terminator 6 11-05-2012 04:19 AM
Tophat - processing several files fastq marb Bioinformatics 3 04-18-2012 03:12 PM
batch editing of ABI files raymoniz General 6 09-29-2010 12:28 PM

Reply
 
Thread Tools
Old 03-04-2013, 04:54 AM   #1
bjoernoest
Member
 
Location: Potsdam

Join Date: Feb 2013
Posts: 11
Default Batch processing of files through tophat etc

If i have a large amount of files i want to run through tophat, htseq and DEseq or other software, do anyone have a neat way (for example a shell script) for doing batch processing so it will start the next run when the previous have finished, so i do not have to start the programs my self with the new parameters?

Bjørn
__________________
Bjørn Øst
bjoernoest is offline   Reply With Quote
Old 03-04-2013, 07:43 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

I have various shell scripts for these sorts of things (I expect that's common). Generally you would need to tailor something like that to whatever your experimental design is and your particular file structure (i.e., where the sequence and annotation files are). If you need some examples to get you started, just send me your email address in a private message and I can send a few examples to you.
dpryan is offline   Reply With Quote
Old 03-05-2013, 12:19 AM   #3
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
Default

For most simple batch processing I often just use a simple bash loop which will run the jobs serially. If you're going to do this a lot you might want to look into adding some error checks and reporting so you can track down what went wrong if it doesn't work. If you want to work on a larger scale you could also look at a proper queueing system, but that's a whole other level of work.

An example of one we did recently to map a pile of fastq files with bowtie would be:

Code:
for i in *.fastq.gz
do zcat $i | bowtie -f -m 1 --strata --best -p 6 --chunkmbs=512 --sam /data/public/Genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37 -  > ${i}.sam
done
simonandrews is offline   Reply With Quote
Old 03-05-2013, 03:14 AM   #4
bjoernoest
Member
 
Location: Potsdam

Join Date: Feb 2013
Posts: 11
Default

Thank you both, that was just what i needed to get started
__________________
Bjørn Øst
bjoernoest 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 11:48 AM.


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