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.
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:
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
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
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
