From 250ee928d998f7112cf419ae80122bada284fb32 Mon Sep 17 00:00:00 2001 From: JannikHamp Date: Mon, 10 Dec 2018 09:36:31 +0100 Subject: [PATCH] Update compareBed.sh --- bin/compareBed.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bin/compareBed.sh b/bin/compareBed.sh index b476a0d..ee65fb4 100644 --- a/bin/compareBed.sh +++ b/bin/compareBed.sh @@ -96,7 +96,7 @@ if [ $he == true ] then echo "This script utilies bedtools to select new footprints from data." echo "Therefore the data is compared with known footprint motifs." - echo "The output is a new .bed file with added sequence information." + echo "The output is a new .bed file with added sequence information and a column with flags for better sequences (1)" echo "Required arguments are data and motifs, both in bed-format, and the fasta genome sequences." echo "If a parameter is chosen, a value must be provided or an error will occur." echo "--------------------" @@ -110,7 +110,7 @@ then echo " " echo " optional parameter:" echo " -w --workdir the path to directory where temporary files will be created" - echo " default is a new directory that is created in the current directory" + echo " default is the current directory" echo " -min --min minimum size of footprints; default is 10" echo " -max --max maximum size of footprints; default is 80" echo " -o --output output path/file ; default dir is workdir and filename is newMotifs.bed and newMotifs.bed.fasta" @@ -258,6 +258,7 @@ else fi #4. remove short/long motivs, make unique ids (relevant for some splitted tfbs from subtract) and handle maxScorePosition +# also creates a small output file with information about the comparison Rscript --vanilla /bin/merge.R $min $max "$workdir" $data