SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Generate .AGP file for WGS submission Tuinhof Bioinformatics 11 11-27-2014 05:59 AM
AGP file from AllPaths-LG Assembly coleoguy Bioinformatics 2 11-14-2013 06:38 AM
How to create .fastq file? sinopnazo Bioinformatics 7 02-01-2013 04:25 AM
Calculating the number of contigs in a scaffold file avtsanger Bioinformatics 5 01-06-2011 01:43 AM
Failure of transforming Velvet .afg file into GDE .contig file ZhigangLi Bioinformatics 0 11-25-2010 06:03 PM

Reply
 
Thread Tools
Old 04-24-2013, 01:49 PM   #1
Wallysb01
Senior Member
 
Location: San Francisco, CA

Join Date: Feb 2011
Posts: 286
Default create scaffold file from contig file and agp file?

Does anyone know how to go from a contig file with the scaffolding information in an AGP file to a full scaffolded multifasta file?

Thanks
Wallysb01 is offline   Reply With Quote
Old 05-10-2016, 01:32 AM   #2
aajosselin
Junior Member
 
Location: Clermont-Ferrand

Join Date: May 2016
Posts: 2
Default

Hi,
did you solve the problem? right now, I have to solve the same problem.
aajosselin is offline   Reply With Quote
Old 05-10-2016, 02:53 AM   #3
Markiyan
Senior Member
 
Location: Cambridge

Join Date: Sep 2010
Posts: 116
Default

If you have contigs with scaffolding info in the agp file -

Than you can pad gaps between the contigs with N's (according to agp file) and write a multifasta file with an entry for each scaffold. Can be done with a bit of perl programming.

(In my case I use newbler output, which includes the scaffolds sequences in the multifasta file).

If you have source reads data, and would like to try a different scaffolder(s) -

have a look at the following review for the scaffolding tools available:

https://genomebiology.biomedcentral....-2014-15-3-r42
Markiyan 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 06:26 PM.


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