From c186bc778f0e784a1c68c515d522e0ae6921c9ec Mon Sep 17 00:00:00 2001 From: saanikat Date: Mon, 8 Apr 2024 13:55:41 -0400 Subject: [PATCH] typo correction, removing .bw from path for reason -the script add *_core.bw to the path --- docs/geniml/tutorials/create-consensus-peaks.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/geniml/tutorials/create-consensus-peaks.md b/docs/geniml/tutorials/create-consensus-peaks.md index 88768ab5..56778007 100644 --- a/docs/geniml/tutorials/create-consensus-peaks.md +++ b/docs/geniml/tutorials/create-consensus-peaks.md @@ -38,12 +38,12 @@ Or we can import it directly into Python: ``` from geniml.universe.cc_universe import cc_universe -cc_universe("tests/consenus/coverage/all_core.bw", +cc_universe("tests/consenus/coverage/", file_out="tests/consenus/universe/universe.bed") ``` Depending on the task we can also smooth the output universe by setting `--merge` -flag with the distance beloved witch peaks should be merged together and +flag with the distance beyond which peaks should be merged together and `--filter-size` with minimum size of peak that should be part of the universe. We can also not use the maximum likelihood cut-off and instead of it use user defined cutoff. For that we have to set `--cutoff` . If we set it to 1 we get union universe, and when to number of files we will get intersection universe. ## Coverage cutoff flexible universe @@ -64,7 +64,7 @@ Or we can import it directly into python: ``` from geniml.universe.ccf_universe import ccf_universe -ccf_universe("tests/consenus/coverage/all_core.bw", +ccf_universe("tests/consenus/coverage/", file_out="tests/consenus/universe/universe.bed") ```