Merge pull request #36 from MoTrPAC/nicolerg-patch-1

Add docs for BAM to bigWig conversion

docs/bam2bigwig.md

@@ -0,0 +1,18 @@
+# BAM to bigWig conversion
+
+The [bigWig file format](https://genome.ucsc.edu/goldenPath/help/bigWig.html) is a convenient way to view dense, continuous data in a genome browser. Follow these steps to convert BAMs to bigWigs for viewing in a genome browser.
+
+### Dependencies 
+- [samtools](http://www.htslib.org/)  
+- [deeptools](https://deeptools.readthedocs.io/en/develop/content/installation.html)  
+
+### Usage 
+1. Download/locate the BAMs you would like to convert.  
+2. For each BAM file, run [bam2bigwig.sh](../scripts/bam2bigwig.sh) as follows: 
+```bash
+bam=/path/to/${viallabel}.Aligned.sortedByCoord.out.bam
+outdir=/path/to/bigwig
+bash bam2bigwig.sh ${bam} ${outdir}
+```
+
+This will generate `${outdir}/${viallabel}.bw`. Each job requires <1G of memory. 

scripts/bam2bigwig.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# convert a single BAM to bigwig format
+# usage: bash bam2bigwig.sh /path/to/90251015803.Aligned.sortedByCoord.out /path/to/bigwigs
+# this command will generate /path/to/bigwigs/90251015803.bw 
+#
+# dependencies: samtools, deeptools
+
+bam=$1
+outdir=$2
+
+prefix=$(basename ${bam} | sed "s/\.Aligned.*//")
+samtools index ${bam}
+bamCoverage -b ${bam} -o ${outdir}/${prefix}.bw