SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Guys, What do you use to trim the Illumina sequences? Daisy-Fu Illumina/Solexa 1 09-15-2011 10:18 AM
Do I need to trim the sequences like this? days369 Bioinformatics 4 08-16-2010 09:19 PM
csfasta quality hard trimming do i need to hard trim the qual file? KevinLam Bioinformatics 2 05-13-2010 03:27 PM
Quality trimmming / Mask low quality bases? bbimber Bioinformatics 9 03-25-2010 02:40 PM
Recommendation for low quality data dawe Bioinformatics 0 11-26-2009 02:02 PM

Reply
 
Thread Tools
Old 07-11-2010, 08:21 PM   #1
biohumin
Junior Member
 
Location: china

Join Date: Jul 2008
Posts: 4
Default How to trim 454 low quality sequences

Hi everybody:
I have got a run of 454 Titanium sequences, however i found there has a few bases whose quality is below 20. Is there has any software to trim the bad bases or sequences? Thank you.
biohumin is offline   Reply With Quote
Old 07-12-2010, 11:04 PM   #2
Jose Blanca
Member
 
Location: Valencia, Spain

Join Date: Aug 2009
Posts: 70
Default

Hi, our ngs_backbone software does that.
Jose Blanca is offline   Reply With Quote
Old 07-13-2010, 04:43 AM   #3
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Why do you want to do the trimming? Isn't the Roche pipeline already trimming off the poor quality bits of the reads?

Where do you want to do the trimming? What I mean is, do you want to work with the SFF file, FASTA+QUAL, or maybe FASTQ files? Would you be interested help to write a python script doing this using Biopython?
maubp is offline   Reply With Quote
Old 07-13-2010, 05:32 AM   #4
Jose Blanca
Member
 
Location: Valencia, Spain

Join Date: Aug 2009
Posts: 70
Default

@maubp

Well, the quality of the sequences released by some 454 services is quite questionable and it is worth to take a look and to trim some more.
If you want to take a look at how ngs_backbone does it you can do it, it's python code and it's based on biopython and on lucy.
Jose Blanca is offline   Reply With Quote
Old 07-13-2010, 09:14 AM   #5
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

@Jose - Understood. I was really wondering if the OP was looking at the untrimmed output from the SFF file (with all the poor quality regions included) rather than the trimmed output (where Roche will have removed most of the rubbish).
maubp 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 08:53 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO