SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Building bfast index with btestindexes bre Bioinformatics 35 09-29-2011 04:34 AM
BFAST index error kursuni Bioinformatics 1 09-27-2011 12:39 AM
bfast index kalinka23 Bioinformatics 1 08-31-2011 06:17 AM
BFAST index set for murines JohnK Bioinformatics 5 06-10-2011 09:14 AM
Bfast index creation guillaum Bioinformatics 3 04-02-2010 08:40 AM

Reply
 
Thread Tools
Old 09-07-2011, 05:59 AM   #1
thurisaz
Member
 
Location: Finland

Join Date: Jun 2011
Posts: 24
Default Index for bfast with Arabidopsis

Hi,

I have an RNA-Seq data set from Arabidopsis (SOLiD, 50+35bp PE) which I would like to try to align with bfast (or bfast+bwa, I guess). I was hoping for some help with building the index -- I don't really know what mask, key size or key width to use. I've had a look at the bfast book and the paper, but I'm still at a bit of a loss. My next step is to read the supplement to the paper in the hope of understanding things well enough to answer these questions, but it occurred to me that someone might been through this before and might be willing to help out.

Does anybody know what indexes would be good to use with A. thaliana? Or maybe some quick pointers to help me figure it out?
thurisaz 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 11:06 AM.


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