Documentation fixes
Small updates to advanced usage docs
@@ -11,10 +11,13 @@ Step 1. Add 500 bp up and downstream of each probe
.. code-block:: bash
- bedtools slop -i probes.bed -b 500 > probes.500bp.bed
+ bedtools slop -i probes.bed -g hg18.genome -b 500 > probes.500bp.bed
+
+NB genome is two column chromosome size list - i.e. https://genome.ucsc.edu/goldenpath/help/hg18.chrom.sizes
Step 2. Get a BED file of all regions not covered by the probes (+500 bp up/down)
+
.. code-block:: bash
bedtools complement -i probes.500bp.bed -g hg18.genome > probes.500bp.complement.bed
@@ -24,8 +27,9 @@ Step 3. Create a masked genome where all bases are masked except for the probes
.. code-block:: bash
- bedtools maskfasta -in hg18.fa -bed probes.500bp.complement.bed -fo \
- > hg18.probecomplement.masked.fa
+ bedtools maskfasta -fi hg18.fa -bed probes.500bp.complement.bed \
+ -fo hg18.probecomplement.masked.fa
+
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