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README.md

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 ================
 
 Pipelines for analyzing padlock-captured DNA sequencing data
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+
+
+Initial configuration:
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+1) Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them)
+
+  e.g. `$ mkdir sequences/hg19; cd sequences/hg19; wget ....fq.gz`
+
+2) Prepare bismark genomic indexes:
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+  e.g. `$ lib/bismark_v0.12.3/bismark_genome_preparation refs/hg19`
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+3) Install necessary scripts:
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+  `$ make install`
+
+
+Running a sample:
+