Hi everyone,
I am also new. I have started to work as a PostDoc in a mutant resequencing project and i am using bowtie for mapping paired end reads against a reference assembly. I would be grateful if someone knows how exactly can i refine aligment options in bowtie in aspects of lenght of match (40%) and similarity levels (70%) for each read in order to relax mapping stringency. I am trying to figure out this and i think is probably something with -n/--seedmms and -e/--maqerr but i am not quite sure.
Any help would be so helpful.
Antonio
I am also new. I have started to work as a PostDoc in a mutant resequencing project and i am using bowtie for mapping paired end reads against a reference assembly. I would be grateful if someone knows how exactly can i refine aligment options in bowtie in aspects of lenght of match (40%) and similarity levels (70%) for each read in order to relax mapping stringency. I am trying to figure out this and i think is probably something with -n/--seedmms and -e/--maqerr but i am not quite sure.
Any help would be so helpful.
Antonio
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