Questions tagged [ribosomal]
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Why do XRAY (but not CryoEM) structures of ribosome in PDB have 2 assemblies?
When i started programming against PDB i had a mixture of confusion & frustration with the fact that certain cif files contain two actual structures aka ...
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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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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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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 ...
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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 ...
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