adding README file for the generation of test data

deeptools · Jul 3, 2017 · 80f35dd · 80f35dd
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commit 80f35dd
Showing 1 changed file with 12 additions and 0 deletions.
diff --git a/hicexplorer/test/test_data/README b/hicexplorer/test/test_data/README
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+# generate restriction sites bed file
+findRestSite --fasta /data/manke/repository/misc/genomes/Dm/dm3/dm3.fa --searchPattern GATC -o DpnII.bed
+
+# make fixed bin size matrix
+hicBuildMatrix -s small_test_R1_unsorted.bam small_test_R2_unsorted.bam -bs 5000  \
+ -o small_test_matrix.h5 --QCfolder QC
+
+# make RF matrix and QC folder
+hicBuildMatrix -s small_test_R1_unsorted.bam small_test_R2_unsorted.bam -rs DpnII.bed  \
+ --restrictionSequence GATC --danglingSequence GATC \
+ --minDistance 150  --maxDistance 1500 -o small_test_rf_matrix.h5 --QCfolder QC_rc
+