I am having difficulties in mapping fast files with longer reads (~150 bp) against short custom reference reads (~21 bp) - I would like to get a proper bowtie like report after the alignment.
Basically, I want to know which read in which fasta files has one of those 21bp reads (ref reads). I would like to try this with
0,1 and 2 mismatches - could anybody help me with this?
I tried with
--local option in
bowtie 2 but it did not work.
my command line:
bowtie2 -a --local -x AB_seq -f 1_S1_L001_R1_001.fasta
Same question with details: