Hi Thanh,
Questions are fine, that is what this mailing list is for. But please do
try to cc the mailing list and start a new thread for new topics when
possible.
To generate a length distribution (among other stats), the tool NGS: QC
and manipulation - FastQC is a quick method.
Take
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
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.
Thanh,
To hopefully be clearer, the part matched is clipped (whole or partial, and
there is even some tolerance for low-frequency mismatches).
I would suggest taking a few sequences out and running the tool on them to try
it out. You could test for both length and mismatch constraints this
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