From 777bd5df436ce676f58a11aa59f79191078f889b Mon Sep 17 00:00:00 2001
From: Nicole Gay <nicolerg@stanford.edu>
Date: Wed, 30 Sep 2020 15:36:23 -0700
Subject: [PATCH 1/3] Create bam2bigwig.md

---
 docs/bam2bigwig.md | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 docs/bam2bigwig.md

diff --git a/docs/bam2bigwig.md b/docs/bam2bigwig.md
new file mode 100644
index 0000000..4d09831
--- /dev/null
+++ b/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} ${outdir}
+```
+
+This will output the bigwig files in `${outdir}`. Each job requires <1G of memory. 

From c366b243a45f6c4010118ff8b85a4f6a74d763b4 Mon Sep 17 00:00:00 2001
From: Nicole Gay <nicolerg@stanford.edu>
Date: Wed, 30 Sep 2020 15:39:11 -0700
Subject: [PATCH 2/3] Create bam2bigwig.sh

---
 scripts/bam2bigwig.sh | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 scripts/bam2bigwig.sh

diff --git a/scripts/bam2bigwig.sh b/scripts/bam2bigwig.sh
new file mode 100644
index 0000000..44b0e20
--- /dev/null
+++ b/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

From 2d0d3733edaa6570d57c0b25fe47d23442b25288 Mon Sep 17 00:00:00 2001
From: Nicole Gay <nicolerg@stanford.edu>
Date: Wed, 30 Sep 2020 15:41:13 -0700
Subject: [PATCH 3/3] Update bam2bigwig.md

---
 docs/bam2bigwig.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/bam2bigwig.md b/docs/bam2bigwig.md
index 4d09831..b6e9dc4 100644
--- a/docs/bam2bigwig.md
+++ b/docs/bam2bigwig.md
@@ -15,4 +15,4 @@ outdir=/path/to/bigwig
 bash bam2bigwig.sh ${bam} ${outdir}
 ```
 
-This will output the bigwig files in `${outdir}`. Each job requires <1G of memory. 
+This will generate `${outdir}/${viallabel}.bw`. Each job requires <1G of memory.