SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Error Bowtie with fastq files (from Solid .csfasta & .qual) pepperoni Bioinformatics 0 10-12-2011 08:20 PM
Spiking phiX into multiplexed libraries as well as barcode sequences cmawhinney Sample Prep / Library Generation 3 09-16-2010 11:13 AM
csfasta quality hard trimming do i need to hard trim the qual file? KevinLam Bioinformatics 2 05-13-2010 02:27 PM
extract subset (mapped reads) from csfasta and .qual files KevinLam SOLiD 1 01-18-2010 12:38 AM
fastq to csfasta and .qual samt SOLiD 15 10-29-2009 09:11 AM

Reply
 
Thread Tools
Old 08-03-2011, 07:12 AM   #1
lei
Member
 
Location: germany

Join Date: Mar 2010
Posts: 14
Default how to separate barcode libraries from csfasta and qual file

anyone knows about how to do that?
Thanks!
lei is offline   Reply With Quote
Old 08-03-2011, 07:34 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

No need to do so. The libraries are already extracted by the machine, at least on the SOLiD 4 and SOLiD 3.
westerman is offline   Reply With Quote
Old 08-03-2011, 10:30 AM   #3
lei
Member
 
Location: germany

Join Date: Mar 2010
Posts: 14
Default

really?I just got one csfasta and qual file including 8 libraries from the core facility. If so, I will ask them tomorrow.
lei is offline   Reply With Quote
Old 08-03-2011, 10:43 AM   #4
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Yes, ask them. Let us know what they say. Since the SOLiD has separate runs for the barcode, the F3 and the F5/R3 then these should separate into three different files and into different samples. We get (and give to our customers) files that are named like:

run00165_Stemredo_BC_000738_StemRedo_05.csfasta
run00165_Stemredo_F5-BC_000738_StemRedo_05.csfasta
run00165_Stemredo_F3_000738_StemRedo_05.csfasta

run00165_Stemredo_BC_000739_StemRedo_06.csfasta
run00165_Stemredo_F5-BC_000739_StemRedo_06.csfasta
run00165_Stemredo_F3_000739_StemRedo_06.csfasta

Plus associated qual and stats files; e.g.,

run00165_Stemredo_BC_QV_000738_StemRedo_05.qual
run00165_Stemredo_BC.stats

Note that there are three .csfasta files per sample.


It is possible to merge all data from the samples into one file. But, at the risk of critiquing another core facility, why do so?
westerman is offline   Reply With Quote
Old 10-21-2011, 06:38 PM   #5
songxifan
Junior Member
 
Location: san diego

Join Date: Sep 2011
Posts: 2
Default

I'm having the same problem. I have four barcoded samples, but only got one csfasta and qual files. Did the ppl got the solution for the problem from ABI?
Thx!
songxifan 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 04:22 PM.


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