SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Sequencing Single-end on DE to save money, good idea? Kate.W Bioinformatics 2 02-21-2013 01:14 PM
ask for idea about de novo genome camelbbs De novo discovery 9 06-15-2012 10:49 AM
a brilliant idea on dna sequencing technology development jagdish78@gmail.com Introductions 0 05-28-2011 09:27 PM
iDEA Conference (June 14-15, 2011, San Diego) illumina Events / Conferences 0 04-06-2011 03:29 PM
Primer removal tool for next gen? Shruti Madhiwalla Bioinformatics 3 03-24-2011 01:37 AM

Reply
 
Thread Tools
Old 09-19-2013, 10:21 PM   #1
arkilis
Senior Member
 
Location: Australia

Join Date: Jul 2013
Posts: 119
Default Any idea on primer trimming tool?

I was looking at some sequence data generated by Sanger Sequencer ABI 3730 xl. Is there any recommended tool to do the primer trimming?

And if it is possible, is there any tool to sequencing trimming, since I want to discard the QC<20.. Thanks
arkilis is offline   Reply With Quote
Old 09-20-2013, 06:52 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

We use 'phred' to do quality trimming from the .abi file. If you already have the sequence & quality then any program that handles both (e.g., in fastq format) should work.
westerman is offline   Reply With Quote
Old 09-22-2013, 12:20 PM   #3
arkilis
Senior Member
 
Location: Australia

Join Date: Jul 2013
Posts: 119
Default

Quote:
Originally Posted by westerman View Post
We use 'phred' to do quality trimming from the .abi file. If you already have the sequence & quality then any program that handles both (e.g., in fastq format) should work.
Thanks for your info!
arkilis is offline   Reply With Quote
Old 09-23-2013, 10:51 AM   #4
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

We have used phred for basecalling and lucy[1] for quality and primer trimming for years. We used cross_match for contamination screening. Lucy 2 has a GUI and is designed for interactive work[2].

[1] = http://lucy.sourceforge.net/
[2 ]= http://www.complex.iastate.edu/downl...cy2/index.html

Last edited by sklages; 09-23-2013 at 10:52 AM. Reason: :-)
sklages is offline   Reply With Quote
Old 09-23-2013, 05:34 PM   #5
arkilis
Senior Member
 
Location: Australia

Join Date: Jul 2013
Posts: 119
Default

Quote:
Originally Posted by sklages View Post
We have used phred for basecalling and lucy[1] for quality and primer trimming for years. We used cross_match for contamination screening. Lucy 2 has a GUI and is designed for interactive work[2].

[1] = http://lucy.sourceforge.net/
[2 ]= http://www.complex.iastate.edu/downl...cy2/index.html
Thanks sklages!

Actually I tried both cmd and gui version. It seems it does not have the option to trim primer. Could u provide one example? Thanks again!

=====================================

And I also tried the Geneious Software, it can do the trimming as well.

Last edited by arkilis; 09-23-2013 at 05:53 PM.
arkilis is offline   Reply With Quote
Old 09-23-2013, 09:54 PM   #6
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

Hmm, "primer trimming" = "vector removal at 5' and 3' end"?
If so, have a look at '-vector'. It takes a vector file in fasta format and a splice site file describing the site where the insert has been cloned into the plasmid or the flanking PCR primers from PCR reaction, depending what kind of sample you have.
Have a look at the man page, where the options, including the format of the splice site file, are described extensively. If you have cDNA sequences it is even capable of trimming polyA/T at the end of reads.
For sanger data it is probably the "tool to go" if you are a on linux and a bit familiar with scripting perl/bash/whatever. It is flexible and very fast.
I don't know if the lucy2 GUI version has the same options as cmd line lucy has. You'll have to check this.

Geneious is nice, GUI-only, not that flexible and not for free.

So as always, it depends on what you wanna do and how much effort you want to put into this .. ;-)
sklages is offline   Reply With Quote
Reply

Tags
primer, quality control, trim

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 07:11 AM.


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