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