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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