Bowtie Illumina paired end reads alignment

[empyrean]

Hello all,

I am new to NGS and trying to align illumina paired end data to a region which is of approximately 100kb where as the sequenced genome is about 1gb. Here i wanted to identify single pairs mapped to end of this region where as its other pair doesnot. How could i achieve this easily? Which is better bowtie or BWA? i used following command in bowtie but not working properly.

 bowtie -t -a -m 5 -S -p 10 -X 600 -1 001.fastq -2 002.fastq --al aligned_out

[empyrean]

can someone help?

[westerman]

When you say that something is "not working" it is useful to the rest of us if you can tell us the error message or other reason the program is not working.

[empyrean]

I should have done that, but now bowtie ran succesfully on my data and gave sam output.

HWI-ST5 1:Y:0:CGAAGT    77      *       0       0       *       *       0       0       ANAANNNNNGGCTCC   ###########   XM:i:0

I got something like the top output in sam format. But i need the information of a read in a pair matches to the reference where as its another pair doesnot. The third column which says * was supposed to be a query_identifier and when i got the reads which are not equal to *, i got all pairs but not singles which map to reference. Can i get this info from bowtie?