rRNA genome

[StevenWingett]

Create a rRNA genome for download (--get_genomes)that comprises multiple species and document this in the config file.

[ahdee]

Hi @StevenWingett I'm confused, just downloaded the genome and it looks like there is only one directory with rRNA and it looks like its all for mouse? Is there one for humans?

FastQ_Screen_Genomes/rRNA
GRCm38_rRNA.1.bt2
GRCm38_rRNA.2.bt2
GRCm38_rRNA.3.bt2
GRCm38_rRNA.4.bt2
GRCm38_rRNA.fa
GRCm38_rRNA.rev.1.bt2
GRCm38_rRNA.rev.2.bt2

[StevenWingett]

Hi,

Thanks for your message. I believe it is indeed only mouse sequences. I intend to add to this list rRNA sequences from other species (human etc.) and then users can download a more diverse range of sequences. This is the intention of tagged enhancement.

Are you aware of a pre-compiled list of such sequences?

Many thanks,
Steven

[ahdee]

Thanks @StevenWingett
I build a hg19 tRNA/rRNA with bowtie2 yesterday. Would you be interested in that? I can send you a link.
A

[StevenWingett]

Hi,

Thanks for that, however I think we need to keep tRNA separate from rRNA. Also when adding new genomes it would be best if we added the latest genome assembly.

I think we need a collection of rRNA only for all the species, and document where/how the sequences were filtered. Do you know a good source of such sequences?

Many thanks,
Steven

[ahdee]

@StevenWingett I used ensembl biomart. I just checked and it has a lot of different organisms including human, mouse, chicken, etc etc. I think depending on how well the organism is studied the results could vary but for the most part, I think, most rodents and primates should be no problem.

[StevenWingett]

Great, thanks. When I get a collection together I'll upload to the public downloads folder. In the meantime, users can put together their own rRNA index files.

All the best,
Steven