Re: [maq-help] Beginner's doubts

[Joel M. <ano...@co...>]

Joseph Fass wrote:
> Hi Iavi,
>
>
> On Wed, May 20, 2009 at 7:58 AM, lavi Birdie <go...@ya... 
> <mailto:go...@ya...>> wrote:
>
>     /.../
>     /
>     /1. Since it took almost a day to complete the matching command
>     for 2 million reads (Single read) which are 35 bps length and with
>     2 mismatches allowed, how to introduce parallelization technique
>     to gain time?
>
> try e.g. 'split -l 4000000 reads.fastq' to split your reads into 1M 
> read chunks, or smaller, then run match (aka map) command on each 
> chunk, then use 'maq merge' to merge the 2 or more maps into one map.
alternatively use maq fastq2bfq -n 1000000 ( as you're using it already 
to make bfq files ), then run as many maq map commands as you have 
processors available, though if  you only have 2million reads of course
that just means run 2 of them.  the merge command isn't parallelizable.  
Just follow the steps in maq.pl easyrun.
  [snip]
>
>
>     4. And my next query is about using -N while running match command
>     as well as mapview command? Will it give a similar output as eland
>     as showing the mismatch position in the read with respect to
>     reference? If so which column in out.aln.txt is corresponding to
>     that value and how to interpret. Any example would be easier to
>     understand. If eland gives the output as 25AT7, that means he
>     first 25 bps are exact matches with the reference, 26th and 27th
>     positions are mismatches and 7bps at the end are exactly matching
>     with the reference. MAQ giving an output as eland
>
I don't use -N either, but you might look at the maq pileup -P all.map 
output to know where the mismatch occured on a read.

joel
>
>
> -- 
> Joseph Fass
> Bioinformatics Programmer
> UC Davis Bioinformatics Core
> joseph.fass -at- gmail.com <http://gmail.com> (professional)
> 970.227.5928 (c)  ||  530.752.2698 (w)
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