Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
MAQ Scores & Quantify maq alignments? AnamikaDarwin Bioinformatics 5 09-19-2015 09:24 AM
MAQ Map/Match Problem Fritz_Doll RNA Sequencing 1 06-03-2012 03:38 AM
What is the difference between "maq match" and "maq map" cliff Bioinformatics 1 11-16-2009 03:13 PM
maq map/match settings in colorspace der_eiskern Bioinformatics 0 07-28-2009 02:10 PM
maq match command Layla Bioinformatics 7 04-22-2009 03:42 PM

Thread Tools
Old 07-07-2010, 01:57 AM   #1
Junior Member
Location: europe

Join Date: Apr 2009
Posts: 1
Default maq match

Dear all

I am looking for a way to get local read alignments for known genome regions. I have solexa an 454 reads available.

I tried blast searches to find matching reads, maq match to align the reads, and Tablet to look at the local alignment. The problem with this approach is that maq match does not align reads at the endings of the reference. Can anybody recommend a (better) way to do a local assembly that would align reads to the endings?
Lobaria is offline   Reply With Quote
Old 07-13-2010, 03:46 AM   #2
Senior Member
Location: Germany

Join Date: May 2010
Posts: 101

What do you mean by "maq match does not align reads at the endings of the reference"? If you mean the ends of chromosomes, you usually have a long stretch of Ns there to which od course nothing will map.
epigen 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 06:31 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO