From d178bd4e76a4e0a342308853126c9075b90ea8a3 Mon Sep 17 00:00:00 2001 From: Hayden Metsky Date: Sat, 20 Jan 2024 17:40:12 -0500 Subject: [PATCH] Add recommended value for -e to README --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 2448da92..376d9077 100644 --- a/README.md +++ b/README.md @@ -158,7 +158,8 @@ Higher values lead to more probes. (Default: 1.0 — i.e., whole genome.) * `-e/--cover-extension COVER_EXTENSION`: Assume that a probe will capture both the region of the sequence to which it hybridizes, as well as COVER_EXTENSION nt on each side of that. This parameter is reasonable because library fragments are generally longer than the capture probes, and its value may depend on the library fragment length. -Higher values lead to fewer probes. +Higher values lead to fewer probes, whereas lower values are more stringent in modeling capture. +Values of around 50 are commonly used and work well in practice. (Default: 0.) * `-i/--identify`: Design probes to perform differential identification. This is typically used with small values of COVERAGE and >1 specified `dataset`s.