From 407938cd126985ede965c2067a96967faaaf2f6e Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Mon, 26 Aug 2024 16:31:07 -0400 Subject: [PATCH] doc options --- docs/index.md | 38 ++++++++++++++++++++++++++++++-------- 1 file changed, 30 insertions(+), 8 deletions(-) diff --git a/docs/index.md b/docs/index.md index f6ec45c..64504e9 100644 --- a/docs/index.md +++ b/docs/index.md @@ -47,17 +47,17 @@ The usage can be provided by passing `-h` at the command line. ``` A fast, accurate and versatile tool for long-read transcript quantification. -Usage: oarfish [OPTIONS] --alignments --output +Usage: oarfish [OPTIONS] --output <--alignments |--reads > Options: --quiet be quiet (i.e. don't output log messages that aren't at least warnings) --verbose be verbose (i.e. output all non-developer logging messages) - -a, --alignments - path to the file containing the input alignments -o, --output location where output quantification file should be written + --single-cell + input is assumed to be a single-cell BAM and to have the `CB:z` tag for all read records -j, --threads maximum number of cores that the oarfish can use to obtain binomial probability [default: 1] --num-bootstraps @@ -67,21 +67,43 @@ Options: -V, --version Print version +alignment mode: + -a, --alignments path to the file containing the input alignments + +raw read mode: + --reads path to the file containing the input reads + --reference path to the file containing the reference transcriptome (or existing index) against which to map + --index-out path where minimap2 index will be written (if provided) + --seq-tech sequencing technology in which to expect reads if using mapping based mode [possible values: ont-cdna, ont-drna, pac-bio, pac-bio-hifi] + --best-n maximum number of secondary mappings to consider when mapping reads to the transcriptome [default: 100] + filters: --filter-group [possible values: no-filters, nanocount-filters] -t, --three-prime-clip - maximum allowable distance of the right-most end of an alignment from the 3' transcript end [default: 4294967295] + maximum allowable distance of the right-most end of an alignment from the 3' transcript end [default: *4294967295] -f, --five-prime-clip - maximum allowable distance of the left-most end of an alignment from the 5' transcript end [default: 4294967295] + maximum allowable distance of the left-most end of an alignment from the 5' transcript end [default: *4294967295] -s, --score-threshold - fraction of the best possible alignment score that a secondary alignment must have for consideration [default: 0.95] + fraction of the best possible alignment score that a secondary alignment must have for consideration [default: *0.95] -m, --min-aligned-fraction - fraction of a query that must be mapped within an alignemnt to consider the alignemnt valid [default: 0.5] + fraction of a query that must be mapped within an alignemnt to consider the alignemnt valid [default: *0.5] -l, --min-aligned-len - minimum number of nucleotides in the aligned portion of a read [default: 50] + minimum number of nucleotides in the aligned portion of a read [default: *50] -d, --strand-filter only alignments to this strand will be allowed; options are (fw /+, rc/-, or both/.) [default: .] + +coverage model: + --model-coverage apply the coverage model + -b, --bin-width width of the bins used in the coverage model [default: 100] + +EM: + --max-em-iter + maximum number of iterations for which to run the EM algorithm [default: 1000] + --convergence-thresh + maximum number of iterations for which to run the EM algorithm [default: 0.001] + -q, --short-quant + location of short read quantification (if provided) ``` ## Input to `oarfish`