From a820066b85550501ac261dddd26c7fca748ed1ad Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Mon, 26 Aug 2024 15:15:35 -0400 Subject: [PATCH] update docs --- docs/index.md | 39 +++++++++++++++++++++++++++++++-------- 1 file changed, 31 insertions(+), 8 deletions(-) diff --git a/docs/index.md b/docs/index.md index 2b884ae..b4a08e0 100644 --- a/docs/index.md +++ b/docs/index.md @@ -12,20 +12,21 @@ Also, please note that `oarfish` is scientific software in active development. (also, the `dev` branch should compile from source at all times so feel free to use it, but let us know if you run into any issues). 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 @@ -35,21 +36,43 @@ 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) ```