Hi Jenny,Thank you.When you put the whole 3' adapter sequence into the Clipper, what will happen to the reads that only contains part of the adapter? Are they considered as not containing the adapter and subsequently non-clipped reads?ThanhOn Thu, Sep 19, 2013 at 8:46 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Thanh,
Just enter the whole adapter sequence. The tool will match what is found in the input sequence and clip. The help graphic on the Clip form itself illustrates this - only one adapter is entered (can be entered) but a variable length is clipped from the input to produce the output.
Thanks for posting this new question to the mailing list. This greatly helps us to track & provide the speediest replies.
Best,
Jen
Galaxy team
On 9/19/13 4:15 PM, Hoang, Thanh wrote:
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 appreciatedThanh
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