downloading human rRNA.fasta
I am trying to download human rRNA.fasta file. do you know where I can find this file? in one of the older post in this forum, someone said this file can be found on the UCSC but I did not manage.
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hector3500 •
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Sara
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There are multiple copies of rDNA repeats (~ 400) in humans and they are on different chromosomes. Each of us may have a different complement.
Complete rDNA human repeat is available: how can i download human ribosomal reference ?
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https://www.gencodegenes.org/human/
Take the
Transcript sequencefasta file and extract whatever you need. You couldgrepforrRNAor use the GTF on the same repository to filter for biotypes etc.Aren't rRNAs not annotated in reference genomes? For OP: I followed this site to generate my list of rRNA sequences.
Yes, so? I am referring to transcriptome fasta file.
Either way, the rRNAs that comprise 45S rRNA (e.g. 18S and 28S) aren't annotated/included. Last I checked, even if you look at where those rRNAs are in the genome on let's say, IGV, you won't see an annotated track.
Using your method, you'll pull out a variety of 5S and 5.8S pseudogenes as well as the 12S and 16S mitochondrial rRNAs but not 18S and 28S which I'm assuming the OP would also want.
Did not know, thanks!
For anyone who finds this who is still looking. The riboseq analysis tool ARF uses the rRNA sequences, and have therefore placed them into a fasta file with the 28S, 5S, 5.8S, and 18S rRNAs. It's very helpful.
https://github.com/fallerlab/ARF/blob/main/rRNAs/4V6X_human_rRNAs.fa