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
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
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