SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
Velveth and velvetg. nareshvasani De novo discovery 2 08-09-2013 09:09 AM
Velveth and velvetg use nareshvasani Bioinformatics 6 08-07-2013 08:19 AM
How to set -max_coverage in velvetg reubennowell Bioinformatics 17 05-09-2013 02:55 PM
Velvetg output files nisha2683 Introductions 0 11-02-2012 11:00 AM
ins_length in velvet kentk Bioinformatics 0 03-01-2012 02:37 AM

Reply
 
Thread Tools
Old 10-07-2013, 05:00 PM   #1
Andres_Gomez
Junior Member
 
Location: Urbana, IL

Join Date: Aug 2013
Posts: 8
Default velvetg ins_length parameter

Hi

I have a very simple question regarding the velvetg command, I really don't know what to provide in the ins_length parameter. My Reads were produced with a HiSeq instrument and are 150nt in length, and the average gDNA fragment size: 400-500nt (range from 150bp to 900bp). I noticed that the reads the example in the metavelvet webpage are 100 bp but then they specify 260 as their ins_length parameter. Also if I let velvetg determine ins_length for me , should I still write that argument in script and just complement with auto?

I'd really appreciate your help, as this is not straight forward from the manual or from web-page and it's the first time I deal with this data.

Thanks

Andy

Last edited by Andres_Gomez; 10-07-2013 at 05:13 PM.
Andres_Gomez is offline   Reply With Quote
Old 11-20-2013, 05:44 AM   #2
chkuo
Member
 
Location: Taiwan

Join Date: May 2010
Posts: 11
Default

The 'ins_length' parameter is for specifying the insert size, so you can use a value between 400 and 500. An easier way is to just leave this out in the initial runs. Velvet will estimate the insert size and report it in the log file. After you get this estimate, you can then specify it in the next run.
chkuo 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 06:16 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO