MAQ Alignment Depth

[AnamikaDarwin]

Hello,

Is it possible to get the alignment depth after one aligns with maq map? I want to compute how many reads align for a defined window size?

Thanks,
Anamika.

[kwebb]

after you align, run

> maq mapcheck ref.bfa project.map >mapcheck.txt

the mapcheck.txt output file lists the "Average depth across all non-gap regions" in the information at the start of the file.

hope this helps!

[AnamikaDarwin]

Hi kwebb,

Thanks for your reply. I am aware of this option. But since, I am looking for read statistics in a given window size, this information is not very useful for me.

I plot the alignment cover in contiguous windows, which comes in handy when I am doing further analysis. For instance, when I do a SNP find, I check to see if regions of high snp density have a corresponding good coverage.

Thanks,
Anamika

[kwebb]

perhaps you can use the SNPfilter command? It allows you to set the read depth in which a SNP can be found and filters out SNPs that do not occur within your acceptable range.

I realize that's not exactly what you want, but may be a way to still gain the information you are looking for.

I'm also struggling with a similar issue - not for SNPs but a pile up of sequences in a suspected repeat region. The only way I can see the read depth is using Maqview and the counter at the bottom of the screen. There must be a way to pull out this information since the Avg Read Depth is estimated for the mapcheck output.

Does anyone else have any suggestions?

[bioinfosm]

Have you tried MAQ's pileup command?

[kwebb]

That's what I'm looking for - not sure how I overlooked it in the manual.

Thank you!