Question: How exactly does MAQ handle mate-pair data
0
gravatar for muraved
12 months ago by
muraved0
United States
muraved0 wrote:

Hi,

I'm trying to align a 3.5K-insert mate-pair library using MAQ 0.7.0. From the man page (http://maq.sourceforge.net/maq-manpage.shtml), it is not quite clear to me how exactly MAQ handles the outward orientation of such reads, and how it distinguished paired-end input from mate-pair input. Do I have to pass the files in reverse order, i.e. R.fq F.fq? Do I have to reverse the sequences within the files? Both? Nothing?

Any help is greatly appreciated :-)

ADD COMMENTlink modified 12 months ago • written 12 months ago by muraved0

Is there a specific reason you are using this relatively ancient aligner?

ADD REPLYlink written 12 months ago by genomax51k

Yes. The way it does consensus calling lends itself to read correction. I'm not so much interested in the alignment itself. Also, old doesn't mean bad ;-)

ADD REPLYlink modified 12 months ago • written 12 months ago by muraved0

I never said MAQ was bad :) I have not used MAQ but perhaps suggestions in this thread may help (Aligning Mate Pair Data )

ADD REPLYlink written 12 months ago by genomax51k

Thanks for the link. I am well aware of several read mappers for MP mapping, I'm really asking specifically about MAQ. I do appreciate your help, though :-)

ADD REPLYlink written 12 months ago by muraved0
0
gravatar for h.mon
12 months ago by
h.mon16k
Brazil
h.mon16k wrote:

The MAQ man page has all the info you want:

-a INT Maximum outer distance for a correct read pair [250]

-A INT Maximum outer distance of two RF paied read (0 for disable) [0]

NOTE: Currently, read pairs from Illumina/Solexa long-insert library have RF read orientation. The maximum insert size is set by option -A. However, long-insert library is also mixed with a small fraction of short-insert read pairs. -a should also be set correctly.

You supply the reads as is, MAQ will guess by orientation and insert-size if they are paired-reads or mate-pairs.

ADD COMMENTlink modified 12 months ago • written 12 months ago by h.mon16k

As you will notice, my question has the exact same link you provided. The specifics I am asking for are not explained on the man page in my opinion. But maybe I'm overlooking something.

ADD REPLYlink written 12 months ago by muraved0
1

Speaking about the manual, did you see this:

Maq cannot align reads longer than 63bp.

Reads this short are rare nowadays, do your reads conform to this length?

ADD REPLYlink written 12 months ago by h.mon16k

Oops... thanks for pointing that out, I must've missed that :-/

ADD REPLYlink written 12 months ago by muraved0

Do I have to pass the files in reverse order, i.e. R.fq F.fq? Do I have to reverse the sequences within the files? Both? Nothing?

In my understanding, you should do nothing, but set -a and -A to reasonable values to your library.

Or you could pre-process you mate-pair files with NxTrim, keep -A 0, and set -a 5000 (or a reasonable maximum, depending on the skills of who prepared the mate-pair libraries).

Or you could pre-process your mate-pairs with NxTrim using the --rf flag, and then set -a 0 -A 5000 for MAQ.

If in doubt, create a small test case, with known proportions of paired-end and mate-pair reads, map the files and examine the results - this should settle your doubts.

ADD REPLYlink modified 12 months ago • written 12 months ago by h.mon16k
0
gravatar for muraved
12 months ago by
muraved0
United States
muraved0 wrote:

Thanks. Hmm, so, there is no input specification of whether it's paired-end or mate-pair. For an input like maq map F.fq R.fq, it simpy checks the relative positions of mapping locations, and accepts F-R as specified by -a, and R-F as specified by -A then?

ADD COMMENTlink written 12 months ago by muraved0
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