Question: Problem with custom reference genome
gravatar for Philipp.rathert
2.6 years ago by
Philipp.rathert30 wrote:

Dear all,

on our local galaxy-docker-stable instance I would like to include additional reference genomes for bowtie to shorten the time for the users.

I downloaded fasta files for mm10 and GRCh38 uploaded to my history and tried to run the bowtie index builder from the local data --> run data manger tools section.

I cannot select the history fasta file to build an index although we can map against the same fasta using bowtie when we provide it in the history.


What am I missing?

Do I have to process the fasta before in any way?


Thank you very much for your help.





bowtie index • 665 views
ADD COMMENTlink modified 2.4 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by Philipp.rathert30
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Sorry, this one was missed. Have you worked out how to use the Data Manager?

It could be that the input fasta datasets were not assigned the datatype "fasta". This is required for the DM tool to recognize the data as appropriate input. To remedy, assign the datatype (pencil icon > Edit Attributes).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 152 users visited in the last hour