SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Problems with STAR alignment tellsparck Bioinformatics 1 05-26-2015 07:02 AM
2nd Pass Alignment with STAR for RNA-sequencing cbaudo RNA Sequencing 3 03-04-2015 04:59 AM
STAR for alignment sbdk82 Bioinformatics 2 09-09-2014 09:22 AM
STAR: Alignment reported with less matches than parameter --outFilterMatchNmin AnneBiton Bioinformatics 0 07-29-2014 12:45 PM
BWA alignment of multiple read files, the order of processing matters? gene_x Bioinformatics 8 07-12-2013 01:20 PM

Reply
 
Thread Tools
Old 10-07-2015, 02:43 PM   #1
graceqy
Member
 
Location: New York City

Join Date: Mar 2012
Posts: 14
Default STAR alignment with multiple fq files

I am trying to do RNAseq PE alignment using STAR. It works for one pair of fq files:

$ STAR --runThreadN 30 --genomeDir /srv/STAR_genome/human/ --readFilesIn /../RNA4_1_R1.fastq.gz /../RNA4_1_R2.fastq.gz --readFilesCommand zcat

However, I have multiple fq files for one sample and I need to align them into one sam file. When I tried to align all together, it returns 'Segmentation fault (core dumped)':

$ STAR --runThreadN 30 --genomeDir /../STAR_genome/human/ --readFilesIn /../RNA4_1_R1.fastq.gz /../RNA4_1_R2.fastq.gz /srv/RNA4_2_R1.fastq.gz /../RNA4_2_R2.fastq.gz --readFilesCommand zcat
Segmentation fault (core dumped)

Could STAR deal with multiple pairs? What am I missing, pls?

Last edited by graceqy; 10-07-2015 at 03:05 PM.
graceqy is offline   Reply With Quote
Old 10-07-2015, 03:05 PM   #2
graceqy
Member
 
Location: New York City

Join Date: Mar 2012
Posts: 14
Default

Sorry I figured it out. But I don't know how to delete the post.
graceqy is offline   Reply With Quote
Old 04-16-2016, 10:32 AM   #3
kristina.gagalova
Junior Member
 
Location: The Netherlands

Join Date: Apr 2016
Posts: 3
Default

Could you please share? Thank you
kristina.gagalova 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 11:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO