From 527d15398e2428813a44750ca34af71d2a2ead77 Mon Sep 17 00:00:00 2001 From: jpsmith5 Date: Fri, 16 Oct 2020 11:49:38 -0400 Subject: [PATCH] update usage --- usage.txt | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/usage.txt b/usage.txt index acfcf2b0..33cea2cd 100644 --- a/usage.txt +++ b/usage.txt @@ -4,15 +4,15 @@ usage: pepatac.py [-h] [-R] [-N] [-D] [-F] [-T] [--silent] [--verbosity V] INPUT_FILES [INPUT_FILES ...] [-I2 [INPUT_FILES2 [INPUT_FILES2 ...]]] -G GENOME_ASSEMBLY [-Q SINGLE_OR_PAIRED] [--aligner {bowtie2,bwa}] - [--peak-caller {fseq,macs2}] [-gs GENOME_SIZE] - [--trimmer {trimmomatic,pyadapt,skewer}] + [--peak-caller {fseq,genrich,hmmratac,homer,macs2}] + [-gs GENOME_SIZE] [--trimmer {trimmomatic,pyadapt,skewer}] [--prealignments PREALIGNMENTS [PREALIGNMENTS ...]] - [--deduplicator {picard,samblaster}] [--TSS-name TSS_NAME] - [--blacklist BLACKLIST] [--anno-name ANNO_NAME] - [--peak-type {fixed,variable}] [--extend EXTEND] - [--frip-ref-peaks FRIP_REF_PEAKS] [--motif] [--sob] - [--no-scale] [--prioritize] [--keep] [--noFIFO] [--lite] - [--skipqc] [-V] + [--deduplicator {picard,samblaster,samtools}] + [--TSS-name TSS_NAME] [--blacklist BLACKLIST] + [--anno-name ANNO_NAME] [--peak-type {fixed,variable}] + [--extend EXTEND] [--frip-ref-peaks FRIP_REF_PEAKS] + [--motif] [--sob] [--no-scale] [--prioritize] [--keep] + [--noFIFO] [--lite] [--skipqc] [-V] PEPATAC version 0.9.7 @@ -41,19 +41,18 @@ optional arguments: Single- or paired-end sequencing protocol --aligner {bowtie2,bwa} Name of read aligner - --peak-caller {fseq,macs2} + --peak-caller {fseq,genrich,hmmratac,homer,macs2} Name of peak caller -gs GENOME_SIZE, --genome-size GENOME_SIZE - MACS2 effective genome size. It can be 1.0e+9 or - 1000000000 or shortcuts:'hs' for human (2.7e9), 'mm' - for mouse (1.87e9), 'ce' for C. elegans (9e7) or 'dm' - for fruitfly (1.2e8), Default:hs + Effective genome size. It can be 1.0e+9 or 1000000000: + e.g. human (2.7e9), mouse (1.87e9), C. elegans (9e7), + fruitfly (1.2e8). Default:2.7e9 --trimmer {trimmomatic,pyadapt,skewer} Name of read trimming program --prealignments PREALIGNMENTS [PREALIGNMENTS ...] Space-delimited list of reference genomes to align to before primary alignment. - --deduplicator {picard,samblaster} + --deduplicator {picard,samblaster,samtools} Name of deduplicator program --TSS-name TSS_NAME Path to TSS annotation file. --blacklist BLACKLIST