I want to change from Bowtie to Bowtie2 since Bowtie2 supportes gapped alignments. Normally I used to following command in Bowtie:
bowtie -k 1 -m 1 -n 1 -p 1 -S --best --strata reference.fa file.fastq file.sam 2>>results.summary -k 1 = report up to 1 valid alignments -m 1 = instructs bowtie to refrain from reporting any alignments for reads having more than 1 reportable alignments. -n 1 = Maximum number of mismatches -p 1 = Launch parallel search threads -S = File to write SAM alignments --best--strata = Specifying --strata in addition to --best causes bowtie to report only those alignments in the best alignment "stratum".
I want to use the same settings in Bowtie2 and add the function to allow for one gap with maximal 2 bp in that specific gap. Can anyone help me with changing the settings?