Question: Download sequences of a set of Transcript clusters form Affimetrix
0
gravatar for morgane.moreau
4.7 years ago by
Australia
morgane.moreau0 wrote:

Hi all, 

I have a set of transcripts cluster IDs from Affimetrix (Human gene 1xST) and I would like to download the sequences to BLAST them. These have no annotations and I 'd like to find annotations where possible. 

Does anyone know an easy way to download the sequences from a list of transcript ID ? I downloaded the transcripts and probesets CSV files but they do not contain the sequences. Is there another file that I didn't see that contain the sequences ?

At the moment I need to look for each cluster in Affimetrix, get the sequence, BLAST it, and start again for next cluster. Surely there is a better way to do that. 

 

Any suggestion would be greatly appreciated. 

Thank you, 

Morgane

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by morgane.moreau0
0
gravatar for morgane.moreau
4.7 years ago by
Australia
morgane.moreau0 wrote:

Never mind, I found out how to do it reasonably quickly. 

For those who like me are starting with microarray and wonder: 

 

You do a customize view in Affimetrix where you can select all the info you want about a cluster. 

 

Then you do a batch query, download the file and BLAST all sequences at once.

 

 

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by morgane.moreau0
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