Convert previous bismark file to new methylsig input

[Yaseswini]

Hi,

We have ERRBS data from previous versions of bismark tool. Sample methylcall file is below -- dat1 chrBase chr base strand coverage freqC freqT

1 chr1.4694 chr1 4694 R 2 100 0 2 chr1.4668 chr1 4668 R 9 100 0 3 chr1.4688 chr1 4688 R 2 100 0 4 chr1.4686 chr1 4686 R 2 100 0 5 chr1.4658 chr1 4658 R 9 88.9 11.1 6 chr1.4701 chr1 4701 R 2 100 0 7 chr1.4673 chr1 4673 R 9 100 0 8 chr1.6347 chr1 6347 R 3 100 0 9 chr1.6339 chr1 6339 R 5 100 0 10 chr1.6321 chr1 6321 R 5 80 20 I wrote the below code to transform into the new input required by methylsig. dat1 = dat dat1$numReads_C = round( dat1$freqC * dat1$coverage )/100 dat1$numReads_T = dat1$coverage - dat1$numReads_C #percent = numReads_C/coverage * 100 dat1$start = as.integer( dat1$base - 1 ) dat1$base = as.integer( dat1$base ) dat1_for_methylsig = dat1[ , c("chr","start","base","freqC","numReads_C","numReads_T") ] Can you please let me know if this is the correct approach or if there is a better way to use my old methylcall file to be able to use the package.. Thanks Yaseswini

[rcavalcante]

Hi Yaseswini,

Yes, this looks correct, and is generally how I would done this too.

Raymond

[Yaseswini]

Great!! Thanks @rcavalcante !