Hi all,
I want to add the strand information on the methylation calls from bismark v0.13 by using the coverage2cytosine script.
Here is an example:
The original methylation calls file (no strand information)
chr1 3000573 3000573 84.6153846153846 22 4
chr1 3000725 3000725 50.7462686567164 68 66
chr1 3000900 3000900 26.3157894736842 5 14
chr1 3001346 3001346 50 2 2
chr1 3001394 3001394 100 2 0
chr1 3002176 3002176 100 3 0
chr1 3002177 3002177 90 9 1
After transforming the data with the coverage2cytosine script I have the information for the strand but the rest of the data are not the same:
chr1 3000574 + 0 0 CG CGG
chr1 3000575 - 0 0 CG CGC
chr1 3000726 + 0 0 CG CGT
chr1 3000727 - 0 0 CG CGC
chr1 3000901 + 0 0 CG CGG
chr1 3000902 - 0 0 CG CGC
chr1 3001346 + 2 2 CG CGT
chr1 3001347 - 0 0 CG CGT
chr1 3001394 + 2 0 CG CGG
chr1 3001395 - 0 0 CG CGC
chr1 3001631 + 0 0 CG CGT
chr1 3001632 - 0 0 CG CGA
chr1 3002177 + 9 1 CG CGG
Do you have any idea of what might happen her?
Thanks in advance,
Anna
I want to add the strand information on the methylation calls from bismark v0.13 by using the coverage2cytosine script.
Here is an example:
The original methylation calls file (no strand information)
chr1 3000573 3000573 84.6153846153846 22 4
chr1 3000725 3000725 50.7462686567164 68 66
chr1 3000900 3000900 26.3157894736842 5 14
chr1 3001346 3001346 50 2 2
chr1 3001394 3001394 100 2 0
chr1 3002176 3002176 100 3 0
chr1 3002177 3002177 90 9 1
After transforming the data with the coverage2cytosine script I have the information for the strand but the rest of the data are not the same:
chr1 3000574 + 0 0 CG CGG
chr1 3000575 - 0 0 CG CGC
chr1 3000726 + 0 0 CG CGT
chr1 3000727 - 0 0 CG CGC
chr1 3000901 + 0 0 CG CGG
chr1 3000902 - 0 0 CG CGC
chr1 3001346 + 2 2 CG CGT
chr1 3001347 - 0 0 CG CGT
chr1 3001394 + 2 0 CG CGG
chr1 3001395 - 0 0 CG CGC
chr1 3001631 + 0 0 CG CGT
chr1 3001632 - 0 0 CG CGA
chr1 3002177 + 9 1 CG CGG
Do you have any idea of what might happen her?
Thanks in advance,
Anna
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