Nextflow Modules
Showing module(s) with keyword "psite"
| Module | Keywords | Description |
|---|---|---|
| nf-core/plastid/make_wiggle | genomics riboseq psite wiggle bedgraph | Create wiggle or bedGraph files from alignment files after applying a read mapping rule (e.g. to map ribosome-protected footprints at their P-sites), for visualization in a genome browser |
| nf-core/plastid/metagene_generate | genomics riboseq psite | Compute a metagene profile of read alignments, counts, or quantitative data over one or more regions of interest, optionally applying a mapping rule |
| nf-core/plastid/psite | genomics riboseq psite | Estimate position of ribosomal P-site within ribosome profiling read alignments as a function of read length |
| nf-core/ribowaltz | riboseq psite genomics | Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data |
| nf-core/rpbp/extractorfprofiles | rpbp orf psite profile riboseq | Build a per-ORF P-site count vector for every candidate open reading frame (ORF) in the catalogue. For each ORF, walks the spliced exons in 3-nucleotide codon steps and counts the P-site positions (read 5'-end coordinate plus the length-specific offset selected upstream) that fall in each codon. Counts are summed across all read lengths that passed the periodicity filter from `rpbp/getperiodiclengthsoffsets`. The resulting per-ORF vectors are the input to Bayesian translation scoring in `rpbp/estimateorfbayesfactors`: a translated ORF should show P-site density concentrated at codon-start positions, while a non-translated region should look flat or noisy. Emitted as a sparse matrix (one row per ORF, columns indexed by codon position). |
| nf-core/rpbp/getperiodiclengthsoffsets | rpbp psite offset filter riboseq | Filter the per-read-length P-site offset table down to the (length, offset) pairs that will actually drive ORF-level scoring. Drops read lengths whose metagene profile is too sparsely populated, or whose periodicity Bayes factor is too low / too uncertain, so that downstream P-site counting only uses read lengths with a clean 3-nucleotide signal. Wraps Rp-Bp's `get_periodic_lengths_and_offsets` Python helper directly. Thresholds are configured via named flags in `ext.args`: `--min-count` (default: 1000), `--min-bf-mean` (default: 5), `--max-bf-var` (default: no limit), `--min-bf-likelihood` (default: 0.5). Defaults mirror `rpbp.defaults.metagene_options`. |
| nf-core/rpbp/selectperiodicoffsets | rpbp psite offset orf riboseq | Pick the single best P-site offset for each read length from the per-(length, offset) Bayes factor table produced upstream. For each read length, the offset with the highest periodicity Bayes-factor mean is selected - this is the offset that, when added to a read's 5' end, is estimated to land closest to the ribosomal P-site (the codon being decoded). Downstream, these offsets are used to convert raw read 5'-end coordinates into P-site positions when counting reads against candidate ORFs. Emits one row per read length (length, best offset, supporting Bayes factor statistics). The next step (`rpbp/getperiodiclengthsoffsets`) filters this table to the high-quality pairs that pass user-specified count / signal thresholds before P-site counting in `rpbp/extractorfprofiles`. |