== Using reduced representation bisulfite sequencing (RRBS) to characterize genomic DNA methylation ==

=== Background ===

    * Seminal [https://academic.oup.com/nar/article/33/18/5868/2401288 paper] to introduce RRBS.  The workflow below illustrates how to use [https://www.bioinformatics.babraham.ac.uk/projects/bismark/ bismark] on the resources at the Whitehead Institute. 

=== Step by step analysis ===

  * **QC**
    * Use [https://www.bioinformatics.babraham.ac.uk/projects/trim_galore Trim Galore] or [http://barcwiki.wi.mit.edu/wiki/SOPs/qc_shortReads another] read trimmer to apply quality filters and remove adapters.
    * See our [http://barcwiki.wi.mit.edu/wiki/SOPs/qc_shortReads QC and preprocessing guidelines] for details on running Trim Galore.
    * When .  A command for Trim Galore  paired end reads using gzipped fastq input can look like:

{{{
bsub trim_galore --paired --rrbs --fastqc -o trimmedReads /path/to/raw/data/reads_1.fq.gz /path/to/raw/data/reads_2.fq.gz
}}}

  * **Quantification of methylation calls**
    * Bismark produces BAM file(s) of aligned reads and methylation calls.
 
{{{
bsub /path/to/bismark/bismark --genome /nfs/genomes/mouse_mm10_dec_11_no_random/bowtie/ -1 trimmedReads_1.fq.gz -2 trimmedReads_2.fq.gz
}}}

    * Comment.
    * Comment.

* **Extract methylation calls**
    * After running bismark...
    * For paired ended data...:

{{{
bsub /path/to/bismark/bismark_methylation_extractor -p --gzip --bedGraph trimmedReads_bismark_bt2_pe.bam 
}}}
    * Comment 1
    * Comment 2