Thank you so much, Jennifer!
Your method is pretty good for filtering the sequences that have "A"
at the 10th base position.But I'm sure if it have employed 10 bp
complementary criterion? For the antisense, the 5' will be T (in
complementary to A). Besides, my library contains other small RNAs.
That's why I concern output files of sense and antisense must have
10bp complementary.
Another quick question, in you regular expression, what does "+" mean?
Thanks!
Zhiqiang
Quoting "Jennifer Jackson" <j...@bx.psu.edu>:
Hi Zhiqiang,
Under the tool group "NGS: QC and manipulation" is a tool named
"Manipulate FASTQ". To filter for sequences containing an "A" at
base position 10 and remove them, use the settings are shown in the
attatched .png. Also listed here:
Click on "Add new Match Reads"
Match Reads by: "Sequence Content"
Sequence Match Type: "Regular Expression", using
^.{9}A.+
Click on "Add new Manipulate Reads"
Manipulate Reads on: "Miscellaneous Actions"
Miscellaneous Manipulation Type: "Remove Read"
This will result in the antisense reads being placed in the output,
minus any antisense that happened to have an A at the 10th base
position, which I am not sure is a concern or not.
To output the sense reads, or rather reads with an A at the 10 base
position, change the regular expression to be:
^.{9}[^A].+
The logic is a bit backwards - you are filtering for what you will
be removing - the opposite will be in the output.
Hopefully this helps! Peter's advice about aligning to the genome
and determining strand/orientation vs known transcripts from the
results is mostly likely your second best choice (and more
complicated). Tools in "Interval Operation" group will be of help if
you go down that path.
Best,
Jen
Galaxy team
On 11/26/12 10:47 AM, Zhiqiang Shu wrote:
Hi, Galaxy users!
I have a question on how to find out sense and antisense sequence.
I've got RNA seq data in the fastq format. The sequences inside are
partially complementary to each other (complementary is 10nt, while
entire is about 30nt). How can I separate these sequences into two
groups: sense and antisense (one thing I know is for the sense
sequence the 10th nucleotide is always "A")?
Thanks a lot!
Best,
Zhiqiang
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--
Jennifer Jackson
http://galaxyproject.org
--------------------------
Zhiqiang Shu/Deng Lab
Department of Biological Science
Florida State University
319 Stadium Dr.
Tallahassee, FL, USA, 32306-4295
z...@bio.fsu.edu
___________________________________________________________
The Galaxy User list should be used for the discussion of
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at usegalaxy.org. Please keep all replies on the list by
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