Add rRNA to gtf

assigned to @tavymi75

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rDNA (ribosomal DNA) Mus musculus https://www.ncbi.nlm.nih.gov/nuccore/bk000964

Thanks @tavymi75 Do you have a similar file for human as well?

Forgot to put that! Here it is,

https://www.ncbi.nlm.nih.gov/nuccore/U13369

@katsanto @devagy74 You can add this as an extra ribosomal chromosome. What do you think?

rRNAs are annotated in RNACentral. We should include these as well.

• script to remove ribosomal based on the mappings (no mapping requirement)(and other types of RNAs) /scicore/home/zavolan/katsanto/PROJECTS/RCRUNCH_ENCODE_eCLIP_transcriptomic/scripts/mk_filter_ribosomal_RNAs.py

• annotation for human non coding RNAs: "/scicore/home/zavolan/katsanto/databases/human/rna_central/homo_sapiens.GRCh38.gff3"

If we decide to use this I can provide some rule as well

@tavymi75 @zavolan what's the status of this?

We have the rRNAs for both mouse and human and we will include them as chromosome in the pipeline. We said will put them in while finalising the rules.

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unassigned @tavymi75

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assigned to @katsanto

changed due date to June 12, 2020

I will implement the RNAcentral approach and allow the user to also selectively remove 'tRNA', 'snRNA' 'rRNA'.

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Decided not to implement anything for now. The effect is not expected to cause any issue in the accuracy of the quantifications.The EM employed by salmon and Kallisto is expected to allocate those reads only to the ribosome regions, in case of multimappers. We can create a custom script to modify the TPMs downstream

closed