[DOCS] update adv usage.

docs/content/advanced-usage.rst

@@ -4,89 +4,98 @@ Advanced usage
 
 
 ==========================================================================
-7.1 Mask all regions in a genome except for targeted capture regions.
+Mask all regions in a genome except for targeted capture regions.
 ==========================================================================
-# Add 500 bp up and downstream of each probe
-::
-  slopBed -i probes.bed -b 500 > probes.500bp.bed
+
+Step 1. Add 500 bp up and downstream of each probe
+
+.. code-block:: bash
+
+  bedtools slop -i probes.bed -b 500 > probes.500bp.bed
   
-# Get a BED file of all regions not covered by the probes (+500 bp up/down)
-::
-  complementBed -i probes.500bp.bed -g hg18.genome > probes.500bp.complement.bed
+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
   
-# Create a masked genome where all bases are masked except for the probes +500bp
-::
-  maskFastaFromBed -in hg18.fa -bed probes.500bp.complement.bed -fo hg18.probecomplement.
-  masked.fa
+
+Step 3. Create a masked genome where all bases are masked except for the probes +500bp
+
+.. code-block:: bash
+
+  bedtools maskfasta -in hg18.fa -bed probes.500bp.complement.bed -fo \
+  > hg18.probecomplement.masked.fa
 
 
 ==========================================================================
-7.2 Screening for novel SNPs.
+Screening for novel SNPs.
 ==========================================================================
-# Find all SNPs that are not in dbSnp and not in the latest 1000 genomes calls
-::
-  intersectBed -a snp.calls.bed -b dbSnp.bed -v | intersectBed -a stdin -b 1KG.bed
-  -v > snp.calls.novel.bed
+Find all SNPs that are not in dbSnp and not in the latest 1000 genomes calls
+
+.. code-block:: bash
 
+  bedtools intersect -a snp.calls.bed -b dbSnp.bed -v | \ 
+  bedtools intersect -a - -b 1KG.bed -v | \
+  > snp.calls.novel.bed
 
 
 ==========================================================================
-7.3 Computing the coverage of features that align entirely within an
-interval.
+Computing the coverage of features that align entirely within an interval.
 ==========================================================================
-# By default, coverageBed counts any feature in A that overlaps B by >= 1 bp. If
-you want to require that a feature align entirely within B for it to be counted,
-you can first use intersectBed with the "-f 1.0" option.
-::
-  intersectBed -a features.bed -b windows.bed -f 1.0 | coverageBed -a stdin -b
-  windows.bed > windows.bed.coverage
+
+By default, bedtools ``coverage`` counts any feature in A that overlaps B 
+by >= 1 bp. If you want to require that a feature align entirely within B for 
+it to be counted, you can first use intersectBed with the "-f 1.0" option.
+
+.. code-block:: bash
+
+  bedtools intersect -a features.bed -b windows.bed -f 1.0 | \
+  bedtools coverage -a - -b \
+  > windows.bed.coverage
 
 
 ==========================================================================
-7.4 Computing the coverage of BAM alignments on exons.
+Computing the coverage of BAM alignments on exons.
 ==========================================================================
-# One can combine SAMtools with BEDtools to compute coverage directly from the BAM
-data by using bamToBed.
-::
-  bamToBed -i reads.bam | coverageBed -a stdin -b exons.bed > exons.bed.coverage
+One can combine ``samtools`` with ``bedtools`` to compute coverage directly 
+from the BAM data by using ``bamtobed``.
+
+.. code-block:: bash
+
+  bedtools bamtobed -i reads.bam | \
+  bedtools coverage -a - -b exons.bed \
+  > exons.bed.coverage
   
-# Take it a step further and require that coverage be from properly-paired reads.
-::
-  samtools view -bf 0x2 reads.bam | bamToBed -i stdin | coverageBed -a stdin -b
-  exons.bed > exons.bed.proper.coverage
 
+Take it a step further and require that coverage be from properly-paired reads.
 
+.. code-block:: bash
 
-==========================================================================
-7.5 Computing coverage separately for each strand.
-==========================================================================
-# Use grep to only look at forward strand features (i.e. those that end in "+").
-::
-  bamToBed -i reads.bam | grep \+$ | coverageBed -a stdin -b genes.bed >
-  genes.bed.forward.coverage
+  samtools view -uf 0x2 reads.bam | \
+  coverageBed -abam - -b exons.bed \
+  > exons.bed.proper.coverage
 
-# Use grep to only look at reverse strand features (i.e. those that end in "-").
-::
-  bamToBed -i reads.bam | grep \-$ | coverageBed -a stdin -b genes.bed >
-  genes.bed.forward.coverage
 
 
-  
 ==========================================================================
-7.6 Find structural variant calls that are private to one sample.
+Computing coverage separately for each strand.
 ==========================================================================
-# :
-::
-  pairToPair -a sample1.sv.bedpe -b othersamples.sv.bedpe -type neither >
-  sample1.sv.private.bedpe
-  
-  
+Use grep to only look at forward strand features (i.e. those that end in "+").
+
+.. code-block:: bash
+
+  bedtools bamtobed -i reads.bam | \
+  grep \+$  | \
+  bedtools coverage -a - -b genes.bed \
+  > genes.bed.forward.coverage
+
+Use grep to only look at reverse strand features (i.e. those that end in "-").
+
+.. code-block:: bash
+
+  bedtools bamtobed -i reads.bam | \
+  grep \-$ | \
+  bedtools coverage -a - -b genes.bed \
+  > genes.bed.reverse.coverage
 
-==================================================================================
-7.7 Exclude SV deletions that appear to be ALU insertions in the reference genome.
-==================================================================================
-# We'll require that 90% of the inner span of the deletion be overlapped by a
-recent ALU.
-::
-  pairToBed -a deletions.sv.bedpe -b ALUs.recent.bed -type notispan -f 0.80 >
-  deletions.notALUsinRef.bedpe
\ No newline at end of file