Soap2 paired end mode

[rahul.m.dhodapkar]

I have been trying to use the SOAP2 aligner in paired end mode with the following command:

./soap -a pair1.fastq -b pair2.fastq -D NCBI36.fa.index -o soap_pe_output.txt -2 soap_se_output.txt -m 100 -x 600

this will appear to work just fine, but then when it outputs, it will only output single end alignments. I tried to remove the -2 parameter (the single end output file) but then I got an Output File Error: Can't Write.

is there anyone using soap2 on paired end reads who has encountered this problem before or has any idea of how to go about solving it? Thanks in advance.

-Rahul Dhodapkar

[rahul.m.dhodapkar]

I think that this problem is related to the fact that my reads are in -FF oreintation, but soap 2 by default looks for FR, does anyone know how to change the orientation expectations of SOAP2?