SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
454 data Assembly editing in GAP5 : Join contigs function kumarS_27 454 Pyrosequencing 0 06-06-2013 02:52 PM
Converting 454 reads to illumina reads empyrean Bioinformatics 3 08-28-2012 08:49 AM
454 Reads correction with Short reads ? yvan.wenger Bioinformatics 3 11-26-2010 04:17 AM
Best tool to map 454 reads onto sanger reads? dan Bioinformatics 3 07-27-2009 08:51 AM
Alignment of ABI solid reads and 454 reads baohua100 Bioinformatics 2 02-23-2009 04:58 PM

Reply
 
Thread Tools
Old 02-09-2015, 09:54 AM   #1
styagi
Junior Member
 
Location: houston

Join Date: Jan 2015
Posts: 5
Default 454 gsAmplicon Editing Reads

Does anyone know how to edit reads after alignment has been done using gsAmplicon software? I want to go back and edit any variants that I know are sequencing errors.
styagi is offline   Reply With Quote
Old 02-09-2015, 10:56 AM   #2
styagi
Junior Member
 
Location: houston

Join Date: Jan 2015
Posts: 5
Default

I just found that there is no function to edit reads on the 454 software. Does anyone know a program that would allow me to edit reads post alignment. I dont want filter out the reads completely, I want to be able to edit the errors and use them for alignment and analysis.
styagi is offline   Reply With Quote
Old 02-10-2015, 06:17 AM   #3
Zaag
Senior Member
 
Location: Amsterdam

Join Date: Nov 2009
Posts: 112
Default

Well if that really is what you want you could go from sff to fasta, alter the fasta and go back to sff. You can use the sfftools/sffinfo provided by Roche.
Zaag is offline   Reply With Quote
Old 02-10-2015, 07:42 AM   #4
styagi
Junior Member
 
Location: houston

Join Date: Jan 2015
Posts: 5
Default

I thought sfftools was only provided with the 454 machine which I dont have. I had my samples sequenced at a core bioinformatics lab.
styagi is offline   Reply With Quote
Old 02-10-2015, 07:49 AM   #5
Zaag
Senior Member
 
Location: Amsterdam

Join Date: Nov 2009
Posts: 112
Default

From what I understand they'll give you the programs you need if you ask nicely:

http://seqanswers.com/forums/showpos...8&postcount=13

I think there also are some open source variants of the tools but I never used them.
Zaag is offline   Reply With Quote
Old 02-10-2015, 08:21 AM   #6
styagi
Junior Member
 
Location: houston

Join Date: Jan 2015
Posts: 5
Default

I will look into that.
thank you for your help!
styagi is offline   Reply With Quote
Old 06-17-2015, 07:42 AM   #7
martin2
Member
 
Location: Prague, Czech Republic

Join Date: Nov 2010
Posts: 40
Default

Quote:
Originally Posted by Zaag View Post
Well if that really is what you want you could go from sff to fasta, alter the fasta and go back to sff. You can use the sfftools/sffinfo provided by Roche.
You can't go back from FASTA/Q and re-create SFF. In theory you could but nobody wrote such code yet. As far as I am aware of the status in biopython, Roche sfftools, flower.
martin2 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 09:24 AM.


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