MAQ alignment

[tsucheta]

Hi,

I have been using MAQ for aligning illumina reads to our reference genome for a while. I have noticed that each short read is shown to align with the genome only once even though it has multiple matching locations. I looked for the manual but did not find any command that will do otherwise i.e; show all the mapping locations for a particular short read.

Thanks

Sucheta

[francois.sabot]

For a multiply repeated sequence MAQ will assign a random position. Eg, you have a sequence matching twice in the genome (equivalent probability of position), in A and B region. Thus MAQ will assign either A or B, randomly, each time it cannot decide between them.
I do not think you can ask for all the positions in MAQ. Look to bowtie for it

Cheers