Report number/fraction of reads mapping to ribosomal RNA, and provide coverage plot(s)

[tomkinsc]

Broad user Andi Gnirke requests outputs reporting number or fraction of reads mapping to ribosomal RNA (both human and microbial), plus possibly coverage plot(s) of the mapping depth.

This could be implemented using the existing workflows, align_and_count (similar to or alongside what we report for synthetic ERCC spike-ins) and align_and_plot. Or maybe we just employ kraken to classify reads using the rRNA databases NCBI distributes for BLAST.

see:

• [Human 45S "supercontig" (28S, 5.8S, and 18S; not 5S)] GL000220.1

• [Human mitochondrial rRNA 12S] MT-RNR1

• [Human mitochondrial rRNA 16S] MT-RNR2

• [Human rDNA contig]U13369

• NCBI-curated set of ribosomal RNA (rRNA) reference sequences

  • [Bacteria and Archaea] https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz
  • [Fungi] https://ftp.ncbi.nlm.nih.gov/blast/db/18S_fungal_sequences.tar.gz
  • [Fungi] https://ftp.ncbi.nlm.nih.gov/blast/db/28S_fungal_sequences.tar.gz
  • https://ftp.ncbi.nlm.nih.gov/blast/db/LSU_eukaryote_rRNA.tar.gz
  • https://ftp.ncbi.nlm.nih.gov/blast/db/LSU_prokaryote_rRNA.tar.gz
  • https://ftp.ncbi.nlm.nih.gov/blast/db/SSU_eukaryote_rRNA.tar.gz

This should be mindful of shared homology, for example:

"a small (~600 bp) region of chromosome 21 (9,826,921–9,827,532; Fig. 3b). BLAST results indicate that this region, and its flanking regions, share homology with ETS1 and 18S but with no other rDNA elements (Fig. 3b)" ¹

Footnotes

1. https://doi.org/10.1038/ncomms5850 ↩