Re: [maq-help] Maq Output interpretation

[Heng Li <lh...@sa...>]

Hello Girish,

On 13 Aug 2008, at 20:42, Girish B wrote:

> Hi there !
>
> I am currently doing some illumina runs but I am having trouble to  
> understand and interpret the outputs( Maq 0.6.8) ( Please checkhttp://paste.pocoo.org/show/82004/) 
> . Of this, I am not sure I can understand the following :
>
> 1-  Why does maq do it in 3 rounds ?

Maq, like Eland, will use 6 filters (by default) in alignment. It  
applies 2 filters on reads in each round.

>
> 2-   [match_core] processing sequence gi|157726890|ref|AC_000152.1| 
> AC_000152 (59656706 bp)... Is this for chromosome 1? Because there  
> seems to be 24 of them.

It depends how you name your reference genome. Currently, the name  
following ">" is "gi|157726890|ref|AC_000152.1|AC_000152". I would  
suggest you change the sequence names in the fasta.

> 3- [mapping_count_single] 7, 11, 16, 33. What does that mean ?

These numbers are used in estimating mapping qualities. You can ignore  
them.

> 4- match_data2mapping] 5 pairs are added afterwards.

In the three scans, Maq may miss a read pair if both ends contain 2  
mismatches in the first 28bp, but maq can find them if both ends are  
uniquely aligned.

>     [match_data2mapping] (2279, 2338) reads are moved to meet paired- 
> end requirement.

Maq change the coordinates of 2279 (for the first read) plus 2338  
(second) reads to meet paired end requirement.

>     [match_data2mapping] quality counts of the first reads: (2,  
> 2277); second reads (5, 2333)

This is a breakdown based on mapping qualities. Here 2 read1 and 5  
read2 with mapping quality >=30 are moved to meet PE requirements.

>     [cal_insert_size] 5255 read pairs counted. insert size:  
> 139.748240 +/- 10.506596

Maq is estimating insert sizes based on confidently aligned reads.

> 5-  [align_candidate] gi|157726890|ref|AC_000152.1|AC_000152: (1, 2,  
> 6) out of 16

Maq is performing Smith-Waterman alignment for 16 pairs. After SW, it  
finds 1 read with insertion, 2 with deletions and 6 without indel.

>     [align_candidate] gi|157728228|ref|AC_000153.1|AC_000153: (0, 1,  
> 5) out of 6
>     [align_candidate] gi|157729478|ref|AC_000154.1|AC_000154: (0, 0,  
> 13) out of 19

On different chromosomes.

>
> 6-  and finally [match_data2mapping] 39592 out of 40180 raw reads  
> are mapped with 38222 in pairs.

Ignore this line.

> --   (total, isPE, mapped, paired) = (40180, 1, 39592, 38222)

This is the final statistics: you have 40180 reads initially with  
39592 mapped and 38222 mapped in proper pairs. Note that in maq-0.6.8,  
the number of mapped reads are slightly overestimated. If one end is  
mapped, but the other end not, maq will count both ends as mapped.

regards,

Heng

>
>
> Many thanks,
>
> Girish B
>
>
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