Bseq reproduce a published table

Question

[kanwarjag]

I am trying to find out how can I get this information for my data- Table S1 of http://www.sciencedirect.com/science/article/pii/S1934590914003932. IN summary- I would like to understand how we can calculate total unique Cpg (or % methylated CpGs) and 1X , 10X coverage etc. I used same tool - Bismark for alignment. Any pointer

Thanks

Answer 1

[Devon Ryan]

I include a CpG coverage program as part of Bison. It'll accept a bedGraph file and a fasta file and tell you the number of CpG covered at any depth between 0 and 255.

Alternatively, if you don't need to know the number of CpGs with 0 coverage then awk would be faster.