Questions tagged [ribosomal]

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Does rRNA depletion protocol give higher number of mapped reads in Intronic regions?

Recently, I have downloaded a publicly available dataset, which are 350 tumor samples. I see the following information from the published paper. They used Ribo Zero Gold and rRNA was depleted. Strand ...
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Removing Ribosomal RNA genes from Drosophila gene counts

Hi I have seen similar questions but I still need clarification on Removing ribosomal RNA genes from a gene counts matrix (Drosophila Melanogaster) Finding a fasta file with only ribosomal genes, I ...
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3answers
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Ribosomal RNA QC quantification using SILVA

I would like to create a simple QC check of RNA-Seq data that simply maps the data to rRNA and then counts the number of reads that map. I've done this manually for human using sequences for 5S, 5.8S,...
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1answer
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Infer the new (Ban et. al) ribosomal nomenlature (ex. uL53 ) from the ribosomal protein's sequence

I'm trying to programmatically construct a name for each protein subchain in any ribosome from Uniprot in accordance with Ban et. al's 2014 proposal (excerpt given below) using PDB's and Uniprot's ...
4
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Why is ribosomal RNA difficult to remove even with Poly(A) selection?

In this answer (actually in a comment), it is stated that: As you've noticed from your own analysis, the ribosomal genes have quite variable expression across cells. They're expressed everywhere, ...
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How to filter ribosomal RNA from scRNA-seq data

I want to filter out ribosomal RNA from scRNA-seq data (downloaded from here). Is there a list of known ribosomal RNA? The only solution I found is SortMeRNA, however it works with raw sequencing ...