SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
cufflinks: input alignment from hisat2 dovah RNA Sequencing 5 05-09-2018 01:09 AM
RSEM with HISAT2 Sbamo RNA Sequencing 8 01-26-2016 05:19 AM
question about hisat2 zhanghao Bioinformatics 3 11-16-2015 05:29 PM
bowtie priduced SAm file does not have RG tags in alignment neha General 3 03-12-2013 02:47 AM
Alignment of Long SAGE tags amit491 Bioinformatics 0 01-14-2009 11:48 PM

Reply
 
Thread Tools
Old 08-05-2016, 05:20 AM   #1
dovah
Member
 
Location: Russia

Join Date: Jul 2014
Posts: 18
Default XS tags in hisat2 alignment

Hi,

I had some troubles running Cufflinks with input mapping from HIsat2 (sam/bam).

Cufflinks man page says that input file should be sorted and contain XS tags. To add the tags, I specified --dta-cufflinks as parameter in for the alignment, following Hisat2 man page. With this parameter, supposedly, " [...] HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.". However, this tag does not appear in every line (read) of the generated bam file.

Is this possible and/or expectable? If you ever encountered this issue before, how could you fix it?

I was thinking to first generate a file like this prior to launch of Cufflinks run:
Code:
samtools view hisat2.sorted.bam | egrep 'XS:A:-|XS:A:+' > XS-Tagged.sorted.sam
What do you think?

Last edited by dovah; 08-05-2016 at 05:23 AM.
dovah is offline   Reply With Quote
Old 08-05-2016, 08:15 AM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

IIRC, Cufflinks only requires XS tags for spliced alignments.
Brian Bushnell is offline   Reply With Quote
Old 08-05-2016, 01:03 PM   #3
dovah
Member
 
Location: Russia

Join Date: Jul 2014
Posts: 18
Default

Ha ok, so it should be fine. Have you ever used Cufflinks on bam file generated by Hisat2 by the way? Because it is taking a huge lot of time. I can spot CPU usage (~99%) but no tmp files in the working directory.
dovah is offline   Reply With Quote
Old 08-05-2016, 01:46 PM   #4
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

Quote:
Originally Posted by dovah View Post
Cufflinks ... is taking a huge lot of time.
Sounds like it's working as expected

Seriously, though, sometimes that can happen if you have super-high coverage over certain reasons... in which case filtering out those regions can help (if you're not interested in them).
Brian Bushnell is offline   Reply With Quote
Old 08-07-2016, 02:00 AM   #5
dovah
Member
 
Location: Russia

Join Date: Jul 2014
Posts: 18
Default

oh thanks Brian. I was so worried :P
dovah is offline   Reply With Quote
Reply

Tags
alignment, bam, cufflinks

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 06:56 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO