No, that's not the output from bowtie2 (if someone told you that, they were wrong), it's the output from bsmooth's methylation extractor (or at least it looks like it). The aligner that you tell bsmooth to use has no effect on the formatting of the methylation file.
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I'll also add that after a bit of checking/memory refreshing, the format you posted isn't from bsmooth but is similar to bedGraph format, just with the strand column removed. Adding a strand (e.g., awk 'BEGIN{OFS="\t"}{print $1,$2,$3,".",$4,$5}' somefile > somefile.bedGraph) should allow you to use bedGraph2BSseq.py from bison. The instructions for loading the resulting files into R are in the README.md file.
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Well, you end up just reading the file into a dataframe, adding a column of "." and writing to a new file in a different order:
Code:d <- read.table("somefile", header=F) d$strand = "." write.table(d[,c(1,2,5,3,4)], file="somefile.new", row.names=F, colnames=F)
Code:library(bsseq) files<- c("sample1.file", "sample2.file", "sample3.file") fl <- lapply(files, function(x) read.delim(x, header=F)) gr <- GRanges(seqnames=Rle(fl[[1]][,1]), ranges=IRanges(start=fl[[1]][,2], end=fl[[1]][,3]), strand=Rle("*", nrow(fl[[1]]))) M <- sapply(fl, function(x) x$[,3]) Cov <- sapply(fl, function(x) x$[,4]) groups = data.frame(row.names=files, condition=c("WT","Mut","Mut")) BS <- BSseq(M=M, Cov=Cov, gr=gr, pData=groups, samplesNames=samples)
Given your apparent newness to R, you might want to take a local course before continuing.
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thank you very much for your help, I´m just starting with R but right now I´m not able to take any course, I will do it during Christmas vacation when I have more time... but I´m pushed to finish this before...
thank you very much again for stealing your time
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I run without errors the code that you wrote me for inserting the column but the output is this:
chr1 564495 1 564496 1
chr1 564501 1 564502 1
chr1 565013 1 565014 1
chr1 565040 1 565041 1
chr1 565262 8 565263 0
chr1 565397 5 565398 1
chr1 565469 2 565470 2
the columns are not tabulated (all the data in the same column), the "." column is not there and the others are not sorted
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