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 On 12/8/13 6:21 PM, 朱师云 wrote:
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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