Hello All,
I am using bowtie2 for mapping illumina reads (100 bp). Since I am trying to align the various different plant lines of same species to the reference genome, I would like to play with the mismatches within each read. Because, I cannot expect the 100 bp of a different plant line to match exactly with the reference genome. Therfore, I was using --score-min option, thereby I can manipulate the alignment score.
For eg, bowtie2 --score-min L,0,-0.3, -x my_ref_index -1 read1.fq -2 read2.fq -S output.bam
The above command allows 5 mismatches (1 mismatch = -6 penalty).
But I am not very sure whether this is the right way to do it. I would really appreciate if anybody can please provide their suggestions. And is the default bowtie2 alignment differs from alignment with --score-min option, other than allowing 5 mismatches?
Thanks!!
I am using bowtie2 for mapping illumina reads (100 bp). Since I am trying to align the various different plant lines of same species to the reference genome, I would like to play with the mismatches within each read. Because, I cannot expect the 100 bp of a different plant line to match exactly with the reference genome. Therfore, I was using --score-min option, thereby I can manipulate the alignment score.
For eg, bowtie2 --score-min L,0,-0.3, -x my_ref_index -1 read1.fq -2 read2.fq -S output.bam
The above command allows 5 mismatches (1 mismatch = -6 penalty).
But I am not very sure whether this is the right way to do it. I would really appreciate if anybody can please provide their suggestions. And is the default bowtie2 alignment differs from alignment with --score-min option, other than allowing 5 mismatches?
Thanks!!
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