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