Hi
I got a sam file output from bowtie2 by choosing option -N (setting number of mismatches allowed in a seed alignment during multis alignment)
I used to following command.
bowtie2 --phred33 -x hg19 -N 1 -I 60 -1 X_R1.fq -2 X_R2.fq -S X.sam
I know that -N option can be set to 0 or 1. I chose N as 1 (one mm allowed). Now I want to obtain the similar output with N=0 option. Will i need to perform the alignment again or any option to filter the sam file with N=1 to make it as obtained using N=0?
Thanks
I got a sam file output from bowtie2 by choosing option -N (setting number of mismatches allowed in a seed alignment during multis alignment)
I used to following command.
bowtie2 --phred33 -x hg19 -N 1 -I 60 -1 X_R1.fq -2 X_R2.fq -S X.sam
I know that -N option can be set to 0 or 1. I chose N as 1 (one mm allowed). Now I want to obtain the similar output with N=0 option. Will i need to perform the alignment again or any option to filter the sam file with N=1 to make it as obtained using N=0?
Thanks