SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
what does "edit distance" mean? efoss Bioinformatics 4 09-30-2013 04:50 AM
Edit distance in BWA Rachelly Bioinformatics 4 05-06-2012 12:19 AM
Edit distance sequence tags available (link within) bcf Sample Prep / Library Generation 1 02-12-2011 05:43 PM
Tophat mean inner distance error for SOLID data repinementer Bioinformatics 0 10-28-2010 07:58 PM
BWA concise format output -edit distance wrong biterbilen Bioinformatics 2 11-06-2009 03:55 PM

Reply
 
Thread Tools
Old 04-26-2010, 08:47 AM   #1
meritxellop
Junior Member
 
Location: barcelona

Join Date: Apr 2010
Posts: 2
Default PEM data: edit distance

I'm trying to use VariationHunter to detect SVs based on PEM data generated by Illumina tech.
One of the parameters required as input for the program is theedit distance per mapped pair, and I have no clue about the meaning of this param. In the examples of the usage file it appears as an integer value ranging from 0 to 4.
Any idea???

Thanks a lot
meritxellop is offline   Reply With Quote
Old 07-04-2010, 09:57 AM   #2
Whinds
Junior Member
 
Location: LA

Join Date: Jul 2010
Posts: 2
Default PEM data: edit distance

As per my knowledge it is 2bp for 36bp read length, 3bp for 50bp read length and 4 bp for 75 bp read length.

But I am not very sure. I replied cause no one else did.

Though I have a question how do you calculate the Avgphred and ProbBased Phred ?
Whinds 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 12:55 AM.


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