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Date: Mon, 9 Dec 2013 06:34:28 -0800
From: jen@bx.psu.edu
To: zhusy88@msn.cn; galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] How to filter the sequences containing not[ATCG] character£¿

Hello,

If the data was in .fastqsanger format, you could use the tool "Manipulate FASTQ", but with .fasta, this is a good way.

But watch your regular expression - test it out on a smaller set to make sure it is doing what you want. I see a "start of the line" character in the middle of your expression ("^"). I see why it could be working, with the prior expression being zero or more (*), but knowing what each character does is generally a good idea. The help on the tool is good as are many web sites, but this is simple. Also, you don't need the // slashes, just enter the expression.

To get you started: I would use something like this, with the Select tool and "Matching":

^..*\t[ATCGatcg]+$

(Only one dot is really required, this is just how I always do it. Adds a bit of a format sanity check into the filter).

Hope this helps!

Jen
Galaxy team

Hi Jen,

As the title, I have a [fasta] file that obtained from a [gtf] file,

>cuff102.1

atcgtaaagggcgat

>cuff103.1

gtcgttgactNNNNNNNNgtc

and I want to get the output like this to filter the sequences that contain any not[ATCG] character?

>cuff102.1

atcgtaaagggcgat

I have a large of sequences to filter. I thought a way that firstly convert the file to [interval] file, and secondly SELECT the line not matching the patten /\t[ATCGatcg]*[^ATCGatcg]/.

Am I right? Or there is a one-step way ?

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