From d1257c9eaa8109f20a27f321a1c9b566b2bf6816 Mon Sep 17 00:00:00 2001 From: Ilya Flyamer Date: Tue, 19 Feb 2019 15:44:09 +0000 Subject: [PATCH] Update README.md --- README.md | 43 ++++++++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 2bc87d8..b76b7ce 100644 --- a/README.md +++ b/README.md @@ -32,12 +32,13 @@ Help message should help you get started to use the tool. It is a single command ``` Usage: coolpup.py [-h] [--pad PAD] [--minshift MINSHIFT] [--maxshift MAXSHIFT] [--nshifts NSHIFTS] [--expected EXPECTED] - [--mindist MINDIST] [--maxdist MAXDIST] - [--excl_chrs EXCL_CHRS] [--incl_chrs INCL_CHRS] - [--subset SUBSET] [--anchor ANCHOR] [--by_window] - [--save_all] [--local] [--unbalanced] [--coverage_norm] - [--rescale] [--rescale_pad RESCALE_PAD] [--size SIZE] - [--n_proc N_PROC] [--outdir OUTDIR] [--outname OUTNAME] + [--mindist MINDIST] [--maxdist MAXDIST] [--minsize MINSIZE] + [--maxsize MAXSIZE] [--excl_chrs EXCL_CHRS] + [--incl_chrs INCL_CHRS] [--subset SUBSET] [--anchor ANCHOR] + [--by_window] [--save_all] [--local] [--unbalanced] + [--coverage_norm] [--rescale] [--rescale_pad RESCALE_PAD] + [--rescale_size RESCALE_SIZE] [--n_proc N_PROC] + [--outdir OUTDIR] [--outname OUTNAME] coolfile baselist positional arguments: @@ -58,10 +59,13 @@ optional arguments: when creating controls --nshifts NSHIFTS Number of control regions per averaged window --expected EXPECTED File with expected (output of cooltools compute- - expected). If None, don't use expected and use randomly - shifted controls - --mindist MINDIST Minimal distance of intersections to use + expected). If None, don't use expected and use + randomly shifted controls + --mindist MINDIST Minimal distance of intersections to use. If not + specified, uses --pad as mindist --maxdist MAXDIST Maximal distance of intersections to use + --minsize MINSIZE Minimal length of features to use for local analysis + --maxsize MAXSIZE Maximal length of features to use for local analysis --excl_chrs EXCL_CHRS Exclude these chromosomes form analysis --incl_chrs INCL_CHRS @@ -80,18 +84,21 @@ optional arguments: table with coordinates, their enrichments and cornerCV, which is reflective of noisiness --local Create local pileups, i.e. along the diagonal - --unbalanced Do not use balanced data - rather average cis coverage - of all regions, and use it to normalize the final - pileups. Useful for single-cell Hi-C data, not - recommended otherwise. + --unbalanced Do not use balanced data. Useful for single-cell Hi-C + data together with --coverage_norm, not recommended + otherwise. --coverage_norm If --unbalanced, also add coverage normalization based on chromosome marginals - --rescale Do not use pad, and rather use the actual feature - sizes and rescale pileups to the same shape + --rescale Do not use centres of features and pad, and rather use + the actual feature sizes and rescale pileups to the + same shape and size --rescale_pad RESCALE_PAD If --rescale, padding in fraction of feature length - --size SIZE If --rescale, this is used to determine the final size - of the pileup, i.e. it ill be size×size + --rescale_size RESCALE_SIZE + If --rescale, this is used to determine the final size + of the pileup, i.e. it ill be size×size. Due to + technical limitation in the current implementation, + has to be an odd number --n_proc N_PROC Number of processes to use. Each process works on a separate chromosome, so might require quite a bit more memory, although the data are always stored as sparse @@ -100,8 +107,6 @@ optional arguments: --outname OUTNAME Name of the output file. If not set, is generated automatically to include important information. - - ``` Currently, `coolpup.py` doesn't support inter-chromosomal pileups, but this is an addition that is planned for the future.