Remapping

[MurielGB]

Hello !

I have Illumina sequences that I have to remap onto the reference genome.
First I want to trim the data according to quality and length using Sickle.
Apparently, the treshold mostly used for quality is 20.

But what about length ???
I beleive that if I keep too short sequences they will map in different places in the reference genome and tgis is not good.
But what treshold use ?
35 ?

I have to say that I have different runs with different read length (from 41 to 84).

Thanks a lot for your help.

Muriel

[dpryan]

It sort of depends on what you intend to do downstream with the data. If you're going to be doing something that doesn't pay attention to MAPQ, then you shouldn't set anything too short (maybe 30 or so?). Otherwise, multimappers will just be ignored anyway due to their very low MAPQs, so 20 or so is probably OK, depending on the genome.

[MurielGB]

Thanks dpryan for your answer.

The aim of the analysis is to call variants.

I plan indeed to check the quality of the mapping if this is what you mean by MAPQ though I don't know yet which software I am gonna use.

[dpryan]

I know that in the case of the UnifiedGenotyper in GATK, the maximum Phred score of a base (used in SNP calling) is capped to the MAPQ, which is a mapping quality (the 5th column in a SAM file). With samtools mpileup, there's the -q option (though its default is 0).

[MurielGB]

OK thanks a lot !