Question: Galaxy with Biomart export on Human GR37 build
0
gravatar for indranipoddar
2.3 years ago by
indranipoddar0 wrote:

Hello,

I am interested to export some sequences (rRNA, mitochondrial RNA etc) with Biomart on human genome build GR37 to Galaxy, but when I tried to use Biomart from Galaxy , it only access Biomart with Human GR38. Please let me know how to access GR37 from Biomart to Galaxy.

Thanks.

galaxy • 583 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by indranipoddar0
0
gravatar for Jennifer Hillman Jackson
2.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Once you go out to Biomart, the content (releases available) represents the data Biomart wants to make available through the default web form. They do have archives. Here is where to look:

  1. http://www.ensembl.org/info/website/archives/index.html
  2. http://grch37.ensembl.org/index.html

Data can be downloaded through their tools (see help/support there) then uploaded to Galaxy using FTP. https://wiki.galaxyproject.org/Support#Get_Data:_Upload_tool_used_with_FTP

Hope this helps & have a great weekend, Jen, Galaxy team

ADD COMMENTlink written 2.3 years ago by Jennifer Hillman Jackson25k
0
gravatar for indranipoddar
2.3 years ago by
indranipoddar0 wrote:

Thanks Jen. I wanted to use Bowtie2 from Galaxy to get un-mapped reads from fastq files to rRNA & mitochondrial sequences. So do I need to run 2 times Bowtie2 at Galaxy , one time on rRNA sequneces and another time mitochondrial sequences. Please let me know.

Thanks, Indrani

ADD COMMENTlink written 2.3 years ago by indranipoddar0

Hello Indrani,

That is one way, but there are others.

You should be able to map to the target species' reference genome first, then filter the mapped results based on reference annotation features and/or chromosome.

This prior post at the main Biostars web site has some good details/discussion about where to find reference annotation for rRNA regions. Mitochondrial mappings can be filtered by chromosome name.

Best, Jen, Galaxy team

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson25k
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