Maq Alignment Coordinates

[AnamikaDarwin]

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.

[ECO]

Hey! I'm not at a computer so i cant verify, but I think it's maq mapview...

[apfejes]

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? (-;

[ECO]

Originally Posted by apfejes

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...

[apfejes]

Well, there go my theories of you being an AI or having a cybernetic implant...

[AnamikaDarwin]

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.

[ECO]

Good luck!

[zee]

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.

[AnamikaDarwin]

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

[xzk421]

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?

[mosamam]

Originally Posted by xzk421

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

[kvarala]

Originally Posted by zee

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?