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--- anthill_sri003 [2019/05/12 22:32] – created tmatejuk
+++ anthill_sri003 [2023/08/01 01:08] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
+==== description ====
+Bedtools is a powerful toolset for genome arithmetic. \\
+About:     developed in the quinlanlab.org and by many contributors worldwide.
+Docs:      http://bedtools.readthedocs.io/
+Code:      https://github.com/arq5x/bedtools2
+==== software version ====
+Version:   v2.26.0
+==== sbatch example ====
+...
+<code>
+#!/bin/bash -l
+#SBATCH --partition=long
+#SBATCH --ntasks=1                  # <--- bedtool uses only one core
+#SBATCH --mem 2048M
+#SBATCH --job-name="bedtools test"
+#test filenames
+#https://s3.amazonaws.com/bedtools-tutorials/web/exons.bed
+#https://s3.amazonaws.com/bedtools-tutorials/web/genome.txt
+BEDFILENAME=exons.bed
+GENOMEFILENAME=genome.txt
+#dir path with test files
+TESTFILEDIR="/home/users/${USER}/bedtools_2.26_test"
+#run cdhit computation and remove output files
+cd ${TESTFILEDIR}
+bedtools genomecov -i data/${BEDFILENAME} -g data/${GENOMEFILENAME} > bedtools_test_`date +%s`.txt
+</code>
+==== performance tests ====
+...
+<code>
+...
+</code>
+----
 FIXME
@@ Line 4: / Line 48: @@
 software
-bedtools : instaled from Ubuntu 16.04 repo (version v2.25.0)
+bedtools : instaled from Ubuntu 16.04 repo (version v2aa.25.0)
 tutorial

CRwiki