Changes between Version 2 and Version 3 of SOPs/RRBS


Ignore:
Timestamp:
05/19/22 15:26:08 (3 years ago)
Author:
twhitfie
Comment:

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  • SOPs/RRBS

    v2 v3  
    33=== Background ===
    44
    5     * 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.
     5    * Reduced-representation bisulfite sequencing (RRBS) is an experimental [https://academic.oup.com/nar/article/33/18/5868/2401288 protocol] to measure and compare genomic methylation patterns.  The experiments use one or multiple restriction enzymes on genomic DNA to produce sequence specific fragments that are subsequently treated with bisulfite and sequenced. The workflow below illustrates how to use [https://academic.oup.com/bioinformatics/article/27/11/1571/216956 bismark] to analyze RRBS data on the resources at the Whitehead Institute.
    66
    77=== Step by step analysis ===
    … …  
    1010    * 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.
    1111    * See our [http://barcwiki.wi.mit.edu/wiki/SOPs/qc_shortReads QC and preprocessing guidelines] for details on running Trim Galore.
    12     * When .  A command for Trim Galore  paired end reads using gzipped fastq input can look like:
     12    * A command for Trim Galore  paired end reads using gzipped fastq input can look like:
    1313
    1414{{{
    … …  
    1717
    1818  * **Quantification of methylation calls**
    19     * Bismark produces BAM file(s) of aligned reads and methylation calls.
     19    * [https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Bismark] produces BAM file(s) of aligned reads and methylation calls.
    2020 
    2121{{{
    … …  
    2323}}}
    2424
    25     * Comment.
    26     * Comment.
     25    * Bismark can (since version 0.6.beta1) use [https://www.nature.com/articles/nmeth.1923 bowtie2] to map short reads to reference genome(s).
     26    * In the command above, bismark will expect to find C-to-T and a G-to-A versions of the reference genome.
    2727
    2828* **Extract methylation calls**