Mapping reads with adapter sequences using MAQ

[seq_GA]

I am trying to test pair end mapping with 3' adpter sequence and please let me know how the alogorithm handles the situation.

The adapter sequence is stored in a text file. The adpter sequence is about 7 bps length. If the paired reads are mapped against the reference genome with option -d which contains 3' adapter, how does the algorithm handle the mapping situation.

Will it just eliminate 7bps found in the reads as contaminants and eliminate the adpter portion of the reaad from mapping?

What if both read1 and read2 does not contain the adapter sequence?

If I am not concerned about the -a option (ie) Maximum outer distance for a correct read pair which has the default value as 250 is not of my concern and how to disable the -a option.

Anyone can explain on how to interpret the outputdata?

Thanks.

[seq_GA]

Hi Can anyone suggest a tool to map pair end reads with adpter sequence? Thanks.