Question: extrect sequences according to a tabular
0
gravatar for olivier.claude
2.0 years ago by
France
olivier.claude30 wrote:

Hello,

 

I have 2 files:

-1 fasta file wich contains around 48000 sequences.

-1 tabular wich contains in the first column the name of the sequence plus a short string (3 letters)

I extracted the lines i needed from the tabular and now i have to extract the sequences from the fasta file according to the lines of interrest from the tabular.

But i didn't found wich tool to use. Any idea?

 

Thanks

 

Olivier.

fasta tabular • 524 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by olivier.claude30
2
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hi Olivier,

Try the tool Compare two Datasets. This does exactly what you want - see the example on the tool form.

To prepare, first run the tool Fasta-to-Tabular on the fasta dataset. Then run Compare. If the you want the result in fasta format again, run the tool Tabular-to-Fasta.

Thanks, Jen, Galaxy team

 

 

ADD COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson23k
0
gravatar for olivier.claude
2.0 years ago by
France
olivier.claude30 wrote:

hello!

thank you for the answer. This is working fine!

Olivier

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by olivier.claude30
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