Question

Convert a bed file to bigBed with rtracklayer

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@dd482574

Last seen 9 months ago

Germany

Dear all,

I am trying to find a way to convert a bed to .bigBed file in R using the rtracklayer Bioconductor package. I have heard that it is possible to do the conversion, but I have not found any other way apart from Kent Utilities.

Any help or guidance is highly appreciated. Thank you for your time

bed bigBed rtracklayer ucsc • 1.2k views

ADD COMMENT • link 17 months ago L ▴ 50

score 1 · Answer 1 · 2022-11-14

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

See ?import.bed and ?export.bb

ADD COMMENT • link 17 months ago James W. MacDonald 65k

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Thank you, James, for the guidance. I have learnt a lot, but I am struggling heavily to export a .bigBed file. I am running from error to error.

Here is a link to the file that I am trying to convert to.bigBed and this is what I am doing

test <-  importBed(paste0(path_bed,"arath_gff_sorted_tmp.bed"), header = FALSE, sep = "\t") %>%               # import the bed file
  as.data.frame() %>%                                                                                 # make it to data frame
   mutate(name=str_replace_all(name,"transcript:","")) %>%                                            # change the name
  GenomicRanges::makeGRangesFromDataFrame(., keep.extra.columns=TRUE,  ignore.strand = FALSE, start.field="chromStart",
                                          end.field=c("chromEnd"))                                    # convert to GRanges

The size of each chromosome is

seqlengths(test) <- c(30427671,26975502,23459830,19698289,18585056,366924,154478) 

Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 4546 out-of-bound ranges located on sequence 5. Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the
  underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information.

I am not sure why these ranges are out of bounds, and then when I try to export it to bigBed, it's a disaster.

export.bb(test, paste0(path_bed,"test"))


Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': error in evaluating the argument 'x' in selecting a method for function 't': invalid color specification "255,0,0"

Any hint or clue on how to move on, is highly appreaciated

ADD REPLY • link 17 months ago L ▴ 50

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If you use rtracklayer (importBed is not a function in rtracklayer), it should be a simple one-liner. Using the example data from ?export.bb, as I don't have a bed file handy

>  test_path <- system.file("tests", package = "rtracklayer")
>   test_bb <- file.path(test_path, "test.bb")
> export.bb(import(test_bb), "whatevs.bb")

It's not clear to me why you are doing all that conversion to a data.frame and back. There are any number of ways you can modify a GRanges object directly, so coercing to and from other data formats is probably not necessary. I also don't use the tidyverse as a general rule, as it's usually IMO a repackaging of things that you could already do, but more easily. For example

mutate(name=str_replace_all(name, "transcript:", ""))

Is, if I understand correctly, the same as

gsub("transcript:", "", name)

And more to the point, you can just do

test <- import(paste0(path_bed,"arath_gff_sorted_tmp.bed"))
test$name <- gsub("transcript:", "", test$name)
seqlengths(test) <- (<vector of seqlens that are longer than what you used, probably>)
export(test, paste0(path_bed, "test.bb"))

Also, the error you get from the validity test is telling you that there are almost 5000 sequences on chromosome 5 that are past the length (18585056) that you specified for that chromosome. Either your chromosome length is wrong, or the bed file is wrong.

The final error looks like a tidyverse collision to me. I am 99.999% sure that there is no function t used in export.bb that has a color specification.

ADD REPLY • link 17 months ago James W. MacDonald 65k

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Thank you so much, James. I have already learnt a lot. I ll study your reply and come back. Thank you again for your time

ADD REPLY • link 17 months ago L ▴ 50