I have 40 fasta files with a read length of ~150. A specific part of these 150 bp long reads should contain ~21 bp specific sequences. I have created a local reference.fa file by these 21 bp sequences and want to perform alignment using bowtie1/bowtie2 to see how many reads do have these specific 21 bp sequences with
I tried using bowtie 1 by these options but the output was zero alignment:
bowtie -v 0 ref -a --best --strata -f *.fasta > bowtie_output .
Based on some forums it seems that bowtie can not handle longer reads against a reference with short reads. Could somebody help me to solve this problem?
I would like to go with
zero mismatches (-v 0) and
-a --best --strata options. If I have to use bowtie2 which options of it can translate the
-v 0 -a --best --strata options in bowtie1?