Hey, guys. I need some help with Bowtie2. It will be great if you can help me.
I am trying to align small RNA seq data to C elegans genome. The pre-processing is ok (good base quality, no adapters, reads are trimmed and etc). But in the alignment step bowtie2 only aligned about 50% of all reads. This is not common. I have used Bowtie2 many times to make this kind of alignments and it always worked well.
The read lenth is about 22nt and the command line used to this mapping was:
bowtie2 -p 4 --very-sensitive-local -x ce11 -U trimmed.fastq -S .sam
Do you know if there are big differences between Bowtie2 Versiosn 2 and Bowtie2 Version 3. I am using version 3 for the first time.
Thank you very much.