SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to separate barcode libraries from csfasta and qual file lei Bioinformatics 4 10-21-2011 06:38 PM
hard disk IOPS dnusol Bioinformatics 0 06-21-2011 04:04 AM
RAM, hard drive requirement for RNA-seq analysis arrchi Bioinformatics 1 03-31-2011 01:14 PM
SAM Format - Hard Clip Bio.X2Y Bioinformatics 7 06-14-2010 11:38 AM
Hard drive questions ymc Bioinformatics 1 04-21-2010 07:23 PM

Reply
 
Thread Tools
Old 05-05-2010, 06:15 PM   #1
KevinLam
Senior Member
 
Location: SEA

Join Date: Nov 2009
Posts: 197
Default csfasta quality hard trimming do i need to hard trim the qual file?

Hi
I need to hard trim 10 bases off the csfasta file and I tried to do the hard trim and quality filter in one step (with the csfasta quality file perl script from solid denovo acc tools)

but I ended up with a filtered csfasta file only with the qual file still as it is.

this is a pain for downstream analysis if i have to convert the filtered csfasta into fastq (with the unaltered qual file)

is there a script that outputs filtered qual file and csfasta in one step?

(failing which I probably have to do the hard trim on csfasta and qual) then do the quality filter.
or write my own script for this.
KevinLam is offline   Reply With Quote
Old 05-05-2010, 10:22 PM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by KevinLam View Post
Hi
I need to hard trim 10 bases off the csfasta file and I tried to do the hard trim and quality filter in one step (with the csfasta quality file perl script from solid denovo acc tools)

but I ended up with a filtered csfasta file only with the qual file still as it is.

this is a pain for downstream analysis if i have to convert the filtered csfasta into fastq (with the unaltered qual file)

is there a script that outputs filtered qual file and csfasta in one step?

(failing which I probably have to do the hard trim on csfasta and qual) then do the quality filter.
or write my own script for this.
The "solid2fastq" program included in the BFAST distribution will allow you to convert CSFASTA/QUAL to FASTQ and trim ("-t INT") from the 3' end of the reads at the same time. You can then use BFAST to align the data .
nilshomer is offline   Reply With Quote
Old 05-13-2010, 02:27 PM   #3
Bueller_007
Member
 
Location: Earth

Join Date: May 2010
Posts: 16
Default

Google "rutgers solid filter". It outputs an updated QV.qual file by default.

I believe the -t and -u options of that script will do what you need, but you'll need to turn off all the other quality-filtering options.
Bueller_007 is offline   Reply With Quote
Reply

Tags
csfasta, filter, perl, solid

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 07:46 PM.


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