Hi all,
I am analyzing miRNA sequencing now. My data is 51bp,
single -ended and ~5 M reads. I want to remove the adapter
sequences from the reads before mapping to the genomes/known
miRNA database.
My 3'
adapter sequence is : 5-AGATCGGAAGAGCACACGTCT-3. I found
that many reads only contain part of the 3' adapter
sequence. I am using FASTX-toolkit to clip it off. How
many bases should I put in the " Enter custom clipping
sequence" ? Because in the output files, I end up with more
reads when putting the whole 3 adapter sequence than putting
only first 8 nt.
Also,
miRNA is about 17-25 nt long, I guess that the rest of the
reads (51-21=30bp) must contain part or whole 5's adapter
sequence or the by-product of mRNA/tRNA degradation. So I
think that I have to trim the 5' adapter as well.
Any
suggestion will be highly appreciated
Thanh