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Old 05-18-2015, 10:46 AM   #1
Location: New York NY

Join Date: May 2015
Posts: 24
Arrow Filtering bowtie2 output sam file by mismatch number

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?

ty23991 is offline   Reply With Quote

alignment bowtie2, mismatch

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