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Question: How to convert the data from .wig file to .table or .csv?
1
gravatar for wql_zcq
4.8 years ago by
wql_zcq • 40
wql_zcq • 40 wrote:

Hi, all I read a data from wig file with import.wig function of rtracklayer package. The class() of this data showed :"UCSCdata". I am failed to write the data to other format with "write.table/csv(XXX,file="XX",sep=" ")". Could you tell me which funtion/methods can convert the data to other format(.txt, .csv or excel)?
chip-seq next-gen R • 3.3k views
ADD COMMENT • link •
modified 4.8 years ago by Alex Reynolds ♦ 31k • written 4.8 years ago by wql_zcq • 40
1
gravatar for Sukhi Singh
4.8 years ago by
Sukhi Singh ♦ 10k
Netherlands
Sukhi Singh ♦ 10k wrote:

Use export.wig from rtracklayer with dataFormat to BED. BED format is text based.
ADD COMMENT • link modified 4.8 years ago • written 4.8 years ago by Sukhi Singh ♦ 10k
0
gravatar for anwesha.ghosh.btech
4.8 years ago by
anwesha.ghosh.btech • 10
anwesha.ghosh.btech • 10 wrote:

Does this bed format contain the signal intensity column?

ADD COMMENT • link written 4.8 years ago by anwesha.ghosh.btech • 10

This question is not directly related to parent thread. You should have asked it in a new thread.
As indicated in this link BED format is plain text and only requires three columns by default (chromosome, chromStart, chromEnd). You could include signal intensity as an optional additional column.

ADD REPLY • link modified 4.8 years ago • written 4.8 years ago by GenoMax ♦ 95k
0
gravatar for Alex Reynolds
4.8 years ago by
Alex Reynolds ♦ 31k
Seattle, WA USA
Alex Reynolds ♦ 31k wrote:

You can convert to BED with wig2bed. BED is a tab-delimited text file:

$ wig2bed < in.wig > out.bed

From there, you can bring it into Excel and re-save as CSV, if you need a different delimiter.

Add the --keep-header option if you want that metadata in the output.
ADD COMMENT • link modified 4.8 years ago • written 4.8 years ago by Alex Reynolds ♦ 31k
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