Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: extrect sequences according to a tabular
0
gravatar for olivier.claude
3.0 years ago by
olivier.claude • 30
France
olivier.claude • 30 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 • 764 views
ADD COMMENT • link •
modified 3.0 years ago • written 3.0 years ago by olivier.claude • 30
2
gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for olivier.claude
3.0 years ago by
olivier.claude • 30
France
olivier.claude • 30 wrote:

hello!

thank you for the answer. This is working fine!

Olivier
ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by olivier.claude • 30
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour