I am kind of new to bioinformatics and I am trying to understand why I have been getting extremely different results when I trim my sequences to 20 bp vs when I use seed length of 20 on bowtie. (sorry if it is a stupid question, but I need to know)
My reads are 75 bp. If I remove adapter sequences and etc and run bowtie using -n 0 -l 20, I get only about 45% of reads aligning to my bacterial genome. If I trim them all down to 20 bp and do the same thing, I get 75% of reads aligned. I thought by limiting the seed to 20 bp, only the first 20 bp would be considered for the alignment with 0 mismatches. Shouldn't that give me a similar result to the trimmed ones? Or is the whole 75 bp considered despite the seed length?
Thank you all for the help!