I would like to align my miRNA library (small RNA) with the genome. I read that trimming is optional prior the alignment depending of the downstream analysis. I would like to do DEG only, and I am considering not trimmed my reads.
I performed the alingment with my untrimmed read by using bowtie1. Around 4-6% os my reads aligned with the genome.
bowtie -n 0 -l 30 -a --best --strata --threads 16 $reference/danRer11 -q reads_file.fastq -S output.sam
I also performed with bowtie2, and I had more aligned reads(33%-60%) even It is still not good alingment result.
bowtie2 -p 2 -q --local -x $reference/danRer11 -U reads_file.fastq -S output.sam
Does someone have a suggestion to improve the alingment?
It seems that bowtie2 is better with --local mode since the soft clipping that it does. But I also consider that the bad bowtie1 result could be due my parameter setting.
Thank you in adavance for your answer! :)
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Untrimmed reads have 76bp in average.