I'd like to map metagenomes (2 x 150 bp reads) against selected genes (500 - 3000 bp in length) using Bowtie2. I expect it might happen often then that reads only map partially as they "go beyond" the reference gene as illustrated in the example below.
Read: CTCGACTGGGGGATCTCGATTTCGTAGACGGCTTGCGGTT... ||||||| |||||||| ||||||| Reference Gene: ...CGTTGACGTTAGAAGGGAAGGACTGGGCGATCTCGACTTCGTAG (end of gene)
I'm wondering if bases of the read that are beyond the end of the gene are treated as mismatches, i.e. penalties are added to the alignment score for these?
My desired behavior would be that the read is treated as if it would be only as long as the overlapping region (27 bases in the above example). Bases on the right end of the read in the example shall be clipped, but not the three bases on the left end of the read.
Does anyone now if this can be set in Bowtie2, or possibly if this is even the default behavior with
I know that there is the
--local mode, but this is not exactly what I want as it may clip also the left three bases of the read. Maybe there are settings I could use in combination with
--local to achieve the desired behavior?