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 appreciated
Thanh



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