Entering edit mode
21 months ago
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Dear all,
I am trying to format CpG methylation calls from R package "methyKit" to simple bed format. Since it is a large file, i can not do it in Excel. I also tried Seqmonk, but it does not allow me to export the data in the format I want. Linux awk/seq might be a good option, but i am new to them as well. Basically, I need to trim "chr" column, add "stop" column, convert "F" to "+" /"R" to "-", and freqC with 2 decimal places.
Best,
"From"
chrBase chr base strand coverage freqC freqT
chr1.339 chr1 339 F 7 0.00 100.00
chr1.183 chr1 183 R 4 0.00 100.00
chr1.192 chr1 192 R 6 0.00 100.00
chr1.340 chr1 340 R 5 40.00 60.00
chr1.10007 chr1 10007 F 13 53.85 46.15
chr1.10317 chr1 10317 F 8 0.00 100.00
chr1.10346 chr1 10346 F 9 88.89 11.11
chr1.10349 chr1 10349 F 9 88.89 11.11
"To"
chr start stop freqc Coverage strand
1 67678 67679 0 3 -
1 67701 67702 0 3 -
1 67724 67725 0 3 -
1 67746 67747 0 3 -
1 67768 67769 0.333333 3 -
1 159446 159447 0 3 +
1 162652 162653 0 3 +
1 167767 167768 0.666667 3 +
1 167789 167790 0.666667 3 +
1 167797 167798 0 3 +
