Go Back   SEQanswers > Bioinformatics > Bioinformatics
Similar Threads
Thread Thread Starter Forum Replies Last Post
Need Help, gap between two contigs formed by mapping ketan_bnf Bioinformatics 1 06-14-2011 11:36 PM
how to remove N (gap) in sequences? chronix De novo discovery 3 03-08-2011 04:31 AM
Gap Problems with Velvet1.0 kbushley De novo discovery 0 01-01-2011 12:08 PM
BWA 0.5.7 Gap Inferrence Bug - fix? bgulko Bioinformatics 6 06-15-2010 02:25 PM
PubMed: Next-generation gap. Newsbot! Literature Watch 2 11-12-2009 12:45 PM

Thread Tools
Old 11-13-2009, 11:40 AM   #1
Location: Pennsylvania

Join Date: Nov 2009
Posts: 13
Default gap penalty in BWA

I have short question about gap penalty in BWA. The manual said that the gap open penalty is 11 and gap extension penalty is 4. Does the first gap position will be charged 11 or 15?
Thank you
Victory is offline   Reply With Quote
Old 01-14-2021, 06:19 AM   #2
Junior Member
Location: Cambridge

Join Date: Nov 2020
Posts: 3

I think those are default penalty weights:

Gap open: cost to make gaps
Gap extension: cost to make gaps bigger
annguyen is offline   Reply With Quote

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 06:51 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO