So I have some very long RNA-seq reads (250nt) and I thought of upping the number of allowed mismatches. 2 is the default I used for 100nt but I thought of going to 5 for 250nt reads (1mismatch/50nt). I will be using Tophat to map these reads.
I am concerned Tophat would put >=3 mismatches in a row (nt next to each other) and I would like to stop that from happening so what I would like to know is if Tophat (and Bowtie) would map such a read and if so, are there any changes in its settings to stop that (other than keeping the mismatches set to 2 as default)?
If I cannot stop this, is there an easy to way to filter such reads out from the BAM/SAM file?