Question: Join separate FASTA files; one which contains flanking regions and one with the regions of interest
1
gravatar for mrn0032
3.3 years ago by
mrn003210
United States
mrn003210 wrote:

I have two separate FASTA files here on Galaxy

1.  The genomic sequence of interest in a FASTA file

2.  The upstream and downstream flanking regions of the sequences of interest in FASTA

Is there a way I can combine these FASTA files so the flanking regions are on either side of the appropriate sequence?  

I also have both of these files in INTERVAL format with their genomic locations.  So if I have to use the INTERVAL format then fetch the genomic sequence again that is another possibility.

ADD COMMENTlink modified 3.3 years ago by Bjoern Gruening4.8k • written 3.3 years ago by mrn003210
2
gravatar for Bjoern Gruening
3.3 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Hi,

try the following:

 1. convert "Fasta to Tabular"

 2. paste your files side by side with "Paste two files side by side"

 3. rearrange your columns, so that the sequences are next to each other with the 'cut' tool

 4. "Merge Columns together" from your sequences

 5. use the 'cut' tool to only have 2 columns, one header one your new sequence

 6. use the "Tabular to Fasta" tool to create a Fasta file

 7. share your workflow with other :)

Hope that helps!

Bjoern

 

ADD COMMENTlink written 3.3 years ago by Bjoern Gruening4.8k
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