SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
RSEM: has anyone tried this? ejcho82 RNA Sequencing 2 09-14-2019 11:08 AM
RSEM and cuffdiff june-chris Bioinformatics 2 03-11-2014 07:30 AM
% divergence default in RepeatMasker rebzzy Bioinformatics 1 08-27-2013 06:30 AM
Default Change in CASAVA / BCL->FASTQ skruglyak Bioinformatics 20 11-19-2012 12:51 PM
bfast default parameters jy123 Bioinformatics 1 06-04-2011 08:42 PM

Reply
 
Thread Tools
Old 03-18-2014, 12:48 PM   #1
LearningBIOINFO
Junior Member
 
Location: USA

Join Date: Mar 2014
Posts: 3
Default Help with RSEM: how to change default phred33 to phred64

Hi all,

When I was using the RSEM to align my reads.fastq to my transcripts.fasta (trinityrnaseq_r2013-02-25/util/RSEM_util/run_RSEM_align_n_estimate.pl), I happened to see this:

bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 --chunkmbs 200 -p 4 -a -m 200 -S TRANS -1

But my fastq used phred64, so is there a way to change the default setting (phred33)? Does it affect much if I used the default setting?

Thanks,
He
LearningBIOINFO is offline   Reply With Quote
Old 03-18-2014, 02:45 PM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

It shouldn't matter much. But if you want to change the quality, you could download BBTools and do this:

reformat.sh in=reads.fastq out=fixed.fastq qin=64 qout=33
Brian Bushnell is offline   Reply With Quote
Old 03-18-2014, 05:43 PM   #3
yueluo
Member
 
Location: Guangzhou China

Join Date: Aug 2013
Posts: 82
Default

From the trinity page--
http://trinityrnaseq.sourceforge.net...stimation.html

Quote:
# To pass additional parameters to rsem-calculate-expression,
# type ' -- ' followed by additional pass-through params
You could try <original command> --phred64-quals
Other parameters can be passed in the same way.
yueluo is offline   Reply With Quote
Old 03-19-2014, 07:03 AM   #4
LearningBIOINFO
Junior Member
 
Location: USA

Join Date: Mar 2014
Posts: 3
Default

Hi Yueluo,
I tried typing --phred64-quals behind my command (../run_RSEM_align_n_estimate.pl/ --transcripts) but it said: Unknown option: phred64-quals.
He
LearningBIOINFO is offline   Reply With Quote
Old 03-19-2014, 01:27 PM   #5
LearningBIOINFO
Junior Member
 
Location: USA

Join Date: Mar 2014
Posts: 3
Default

Brian,
I will try it and see if it works.
Thanks,
He
LearningBIOINFO is offline   Reply With Quote
Old 03-19-2014, 09:20 PM   #6
yueluo
Member
 
Location: Guangzhou China

Join Date: Aug 2013
Posts: 82
Default

Well I guess you could follow what Brian suggested. But it is strange you can't use the '--phred64-quals' option as it is mentioned on both trinity's and RSEM's websites.

Converting the phred-qual isn't too difficult, but it is time-consuming when you process large data sets and adds pressure to the system's I/O and storage -- which is a concern to myself and probably some others.
yueluo is offline   Reply With Quote
Old 03-19-2014, 09:33 PM   #7
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

Quote:
Originally Posted by yueluo View Post
Converting the phred-qual isn't too difficult, but it is time-consuming when you process large data sets and adds pressure to the system's I/O and storage -- which is a concern to myself and probably some others.
So you would think! But no, reformat.sh is extremely fast, clocked at over 500MB/s (note that a single HDD won't be able to deliver this). And you can pipe it, like this:

reformat.sh in=reads.fq out=stdout.fq qin=64 qout=33 | someOtherProcess

...which will add no load to the system's I/O or storage, as long as the other process accepts stdin. For, you see, I am also concerned with these things!
Brian Bushnell is offline   Reply With Quote
Old 03-19-2014, 10:21 PM   #8
yueluo
Member
 
Location: Guangzhou China

Join Date: Aug 2013
Posts: 82
Default

Good to hear Brian ! I'll give it a go soon and see how well that goes
yueluo is offline   Reply With Quote
Reply

Tags
phred33, phred64, rsem

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 02:23 AM.


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