Conversion between .bedGraph or .bw to 7-column format
Hello,
I have DNA methylation files that have a 4 column format and come in pairs for percentage (pct) and coverage (cvg), respectively:
con@e:~/Documents/Simmons/DNA_Methylation$ head -5 Merged_9966/bs_seeker-CG.pct.bedGraph
chr1 767 768 0.466666666666667
chr1 845 846 0.142857142857143
chr1 3235 3236 0
chr1 3303 3304 0.962962962962963
chr1 3929 3930 1
con@e:~/Documents/Simmons/DNA_Methylation$ head -5 Merged_9966/bs_seeker-CG.cvg.bedGraph
chr1 767 768 15
chr1 845 846 7
chr1 3235 3236 7
chr1 3303 3304 27
chr1 3929 3930 7
I wrote a perl script to convert this into a 7 column CpG methylation format output by programs like Bismark:
chrBase chr base strand coverage freqC freqT
chr1.17158 chr1 17158 F 15.0 50.0 50.0
chr1.17309 chr1 17309 F 15.0 81.8 18.2
chr1.17334 chr1 17334 F 15.0 78.3 21.7
chr1.178185 chr1 178185 R 15.0 69.4 30.6
However, I made some unknown error in the conversion.
I have 2 questions:
- What is this format called?
- Is there a way I can convert the previous 2 files (.bedGraph) into this second format?
thanks,
-DEC
1 answer
- That format has no name, it's a purely random format.
- The best solution would be a short perl or python script, though you could also use join and awk if you really wanted.
A better route would be to use a generic methylation extractor, like PileOMeth. It outputs in the modified bedGraph format that bismark (among others) uses. That will give you the raw counts, so you don't have to deal with rounding back to the appropriate integer.
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