Question: Is there a way to have bowtie2 give an alignment a score boost if specific regions of the read mapped perfectly? For example, say I have a 24nt read and I am using bowtie2 in –very-sensitive-local mode, if there is a match from positions 2-8 (from the 5' end of my read) I want the match score to be +4, and any match outside of those positions gets the default match score of +2. Is this possible?
Context of my question: I have a sRNA-Seq dataset for Tetrahymena thermophila and I am trying to predict the targeted genes from a class size of siRNAs. Given that Tetrahymena does not have a scRNA database such as miRBase I plan to align the reads to genome looking for alignments to a given gene or its UTRs. As supported by this paper bowtie2 with the --very-sensitive-local parameter is the best option to use. Findings have shown that specific regions of sRNAs (miRNAs, siRNAs, etc.) dictate a sRNA-mRNA interaction more than others (see this paper). Thus, I would like to fine-tune the alignment scoring options if possible.