SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
coordinates in alignment m_elena_bioinfo Bioinformatics 1 01-21-2011 06:07 AM
MAQ and quality scores during alignment warrenemmett Bioinformatics 3 09-27-2010 04:39 AM
MAQ - colorspace alignment troubles Jonathan Bioinformatics 1 01-20-2010 10:16 PM
MAQ alignment tsucheta Bioinformatics 1 01-08-2010 06:58 AM
MAQ Alignment Depth AnamikaDarwin Bioinformatics 5 01-07-2009 11:55 AM

Reply
 
Thread Tools
Old 02-21-2009, 11:43 AM   #1
AnamikaDarwin
Member
 
Location: Boston

Join Date: Nov 2008
Posts: 26
Question Maq Alignment Coordinates

I have used maq to align a set of illumina reads to a reference assembly. Is there a way to directly get the alignment coordinates for the reference assembly?

Thanks,
Anamika

PS, I had inadvertently posted the above question in a different section.
AnamikaDarwin is offline   Reply With Quote
Old 02-21-2009, 11:56 AM   #2
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

Hey! I'm not at a computer so i cant verify, but I think it's maq mapview...
ECO is offline   Reply With Quote
Old 02-21-2009, 12:22 PM   #3
apfejes
Senior Member
 
Location: Oakland, California

Join Date: Feb 2008
Posts: 236
Default

I believe ECO is right. It's "maq mapview filename.map" to display a binary .map file into a human readable format. I usually end up piping it to less so that it doesn't scroll by at unreadable speeds.

Still, I have to wonder, ECO, If you're not at a computer, how did you post that? (-;
__________________
The more you know, the more you know you don't know. —Aristotle
apfejes is offline   Reply With Quote
Old 02-21-2009, 12:27 PM   #4
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

Quote:
Originally Posted by apfejes View Post
I believe ECO is right. It's "maq mapview filename.map" to display a binary .map file into a human readable format. I usually end up piping it to less so that it doesn't scroll by at unreadable speeds.

Still, I have to wonder, ECO, If you're not at a computer, how did you post that? (-;
iPhone != computer in most senses...
ECO is offline   Reply With Quote
Old 02-21-2009, 12:28 PM   #5
apfejes
Senior Member
 
Location: Oakland, California

Join Date: Feb 2008
Posts: 236
Default

Well, there go my theories of you being an AI or having a cybernetic implant...
__________________
The more you know, the more you know you don't know. —Aristotle
apfejes is offline   Reply With Quote
Old 02-21-2009, 12:38 PM   #6
AnamikaDarwin
Member
 
Location: Boston

Join Date: Nov 2008
Posts: 26
Thumbs up maq mapview right solution

Thanks Eco. Once I ran it with the -b option ( the read sequence and the quality are not displayed).

From this output, I plan to get the coordinates of those regions that did not align (roughly about ~15% of the assembly.)

Cheers,
Anamika.
AnamikaDarwin is offline   Reply With Quote
Old 02-21-2009, 12:48 PM   #7
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

Good luck!
ECO is offline   Reply With Quote
Old 02-22-2009, 10:34 PM   #8
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

Anamika,

It would help if you checked the coverage of your reads on the assembly using maq.

First assemble the reads into a consensus:

0) merge all your reads into a single .map file
1) maq assemble output.cns genome.bfa reads.map &> asm.log
2) maq cns2win -w 10000 output.cns > windows.csv

If you plot columns 6 & 7 you get an indication of read depth and coverage of your sequences against the genome.

Hope this helps you out.
zee is offline   Reply With Quote
Old 03-03-2009, 07:53 AM   #9
AnamikaDarwin
Member
 
Location: Boston

Join Date: Nov 2008
Posts: 26
Default

Hi Zee,

I use the option you suggest to get the read depth for the SNP data. However, my aim is to get those coordinates of the assembly that did not align with my input reads. I have about ~15% not aligning.

Thanks,
Anamika
AnamikaDarwin is offline   Reply With Quote
Old 03-03-2009, 11:25 PM   #10
xzk421
Junior Member
 
Location: Beijing,China

Join Date: Jan 2009
Posts: 4
Default maq

hello,
when using MAQ, after the command :
./maq map 1131.map onecdna.bfa coli.bfa
the sreen print:
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 35.
Segmentation fault


what the "Segmentation fault" mean?
xzk421 is offline   Reply With Quote
Old 03-31-2009, 05:16 AM   #11
mosamam
Junior Member
 
Location: uk

Join Date: Jan 2009
Posts: 1
Default

Quote:
Originally Posted by xzk421 View Post
hello,
when using MAQ, after the command :
./maq map 1131.map onecdna.bfa coli.bfa
the sreen print:
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 35.
Segmentation fault


what the "Segmentation fault" mean?

It means that you have not defined you data path
mosamam is offline   Reply With Quote
Old 04-07-2009, 10:09 PM   #12
kvarala
Junior Member
 
Location: Illinois

Join Date: Nov 2008
Posts: 5
Default

Quote:
Originally Posted by zee View Post
Anamika,

It would help if you checked the coverage of your reads on the assembly using maq.

First assemble the reads into a consensus:

0) merge all your reads into a single .map file
1) maq assemble output.cns genome.bfa reads.map &> asm.log
2) maq cns2win -w 10000 output.cns > windows.csv

If you plot columns 6 & 7 you get an indication of read depth and coverage of your sequences against the genome.

Hope this helps you out.
The read depth in column 6 is easy enough to understand but what does the value in column 7 mean? My best guess is that it gives the average mapping quality for that region. Is that even close?
kvarala 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 10:21 PM.


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