Question: Ribo-seq rRNA and other contaminants Fasta file for S. pombe
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gravatar for hdmagpantay
2.8 years ago by
hdmagpantay0 wrote:

Hi everyone, I'm new to Ribo-seq and is working on S. Pombe, our lab has a fasta file for all the contaminants (rRNA, tRNA, etc.) for S. Cerevisiae but we don'w have one for Pombe. I'm wondering which database I can download that? Thank you very much for your help.

ADD COMMENTlink modified 2.8 years ago by genomax84k • written 2.8 years ago by hdmagpantay0
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gravatar for Sej Modha
2.8 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

I am not sure about the specific organisms but it'd be worth looking at SILA rRNA databases: https://www.arb-silva.de/

ADD COMMENTlink written 2.8 years ago by Sej Modha4.7k
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gravatar for genomax
2.8 years ago by
genomax84k
United States
genomax84k wrote:

You should be able to find all data you need from Ensembl Pombe page. GFF3 file has the locations for all rRNA/tRNA etc. Fasta genome sequence is also available from this page.BEDtools getfasta with this gff3 file should get you sequences you need.

ADD COMMENTlink written 2.8 years ago by genomax84k
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