Software suggestion for RRBS DMR (methylation) analysis?

Question

[Whoknows]

Hi all,

I have got a project on WGBS-RRBS data which preprocessed and I have no idea about softwares they have used, I just post some line here and let me know your opinion what software or R package I could use for DMR analysis/ downstream of these data:

Please let me know:

1- What are these columns ( header) exactly?

2- Which softwares/package I could use in the next steps?

Thanks.

track name=WGBS.10 type=bedDetail description="CG methylation level" visibility=3
1       3012517 3012518 50.00   2       +       3012517 3012518 90,150,0        0       0
1       3016106 3016107 100.00  1       -       3016106 3016107 210,0,0 0       0
1       3020793 3020794 100.00  2       +       3020793 3020794 210,0,0 0       6
1       3020794 3020795 50.00   6       -       3020794 3020795 90,150,0        0       2
1       3020813 3020814 100.00  2       +       3020813 3020814 210,0,0 0       6
1       3020814 3020815 83.33   6       -       3020814 3020815 180,60,0        0       2
1       3020891 3020892 0.00    2       -       3020891 3020892 0,240,0 0       0
1       3020945 3020946 0.00    2       -       3020945 3020946 0,240,0 0       0
1       3027398 3027399 0.00    4       -       3027398 3027399 0,240,0 0       0
1       3029228 3029229 41.67   12      +       3029228 3029229 90,150,0        0       0
1       3035641 3035642 33.33   6       +       3035641 3035642 60,180,0        0       0
1       3046232 3046233 50.00   2       +       3046232 3046233 90,150,0        0       0
1       3046316 3046317 100.00  2       +       3046316 3046317 210,0,0 0       0
1       3047027 3047028 100.00  1       -       3047027 3047028 210,0,0 0       0
1       3053738 3053739 71.43   7       +       3053738 3053739 150,90,0        0       0
1       3053896 3053897 42.86   7       +       3053896 3053897 90,150,0        0       0
1       3053963 3053964 71.43   7       +       3053963 3053964 150,90,0        0       0
1       3054809 3054810 100.00  1       +       3054809 3054810 210,0,0 0       0
1       3054852 3054853 100.00  1       +       3054852 3054853 210,0,0 0       3
  

Answer 1

[Shalu Jhanwar]

As you're interested in the identification of DMRs, you can also consider methylKit implemented in R. Full documentation at https://bioconductor.org/packages/devel/bioc/vignettes/methylKit/inst/doc/methylKit.html

Answer 2

[anairlema]

it's seems to be the methyldackel output in which you input your sorted bam from Bismark and get this file with CpG resolution in which each line consists of 6 tab separated columns:

1.The chromosome/contig/scaffold name 2.The start coordinate 3.The end coordinate 4.The methylation percentage rounded to an integer 5.The number of alignments/pairs reporting methylated bases 6.The number of alignments/pairs reporting unmethylated bases

In your case it seems that you have:

1.The chromosome/contig/scaffold name 2.The start coordinate 3.The end coordinate 4.The methylation percentage rounded to an integer 5. coverage 6.strand and again start and end positions.....I don't know why but you can check methyldackel.

Anyway you can input this file on methylsig for the analysis or use bsseq

Hope this can help!