add jar file to make contact matrices from raw HiC data in 2009

BDM-Lab · Dec 8, 2017 · f7db508 · f7db508
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diff --git a/make_input/MakeInput.jar b/make_input/MakeInput.jar
diff --git a/make_input/readme.txt b/make_input/readme.txt
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+This jar file is used to create contact matrices in sparse matrix format. Contact matrices are normalized by ICE normalization.
+This program is implemented for data from this GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM455133
+
+Run the program as follow:
+> java -jar MakeInput.jar chr_id resolution output_file input_files
+
+chr_id: chromosome id (e.g 1,2,3 ...)
+resolution: size of bins
+output_file: an output file
+input_files: a list of input files (separated by space)
+
+Example:
+> java -jar MakeInput.jar 1 1000000 chr1_1mb.txt input\GSE18199_RAW\GSM455137_30305AAXX.1.maq.hic.summary.binned.txt input\GSE18199_RAW\GSM455138_30305AAXX.2.maq.hic.summary.binned.txt
+