Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: How to convert the data from .wig file to .table or .csv?
1
gravatar for wql_zcq
3.0 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 • 1.9k views
ADD COMMENT • link •
modified 3.0 years ago by Alex Reynolds ♦ 28k • written 3.0 years ago by wql_zcq • 40
1
gravatar for Sukhdeep Singh
3.0 years ago by
Sukhdeep Singh ♦ 9.7k
Netherlands
Sukhdeep Singh ♦ 9.7k wrote:

Use export.wig from rtracklayer with dataFormat to BED. BED format is text based.
ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by Sukhdeep Singh ♦ 9.7k
0
gravatar for anwesha.ghosh.btech
3.0 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 3.0 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 3.0 years ago • written 3.0 years ago by genomax ♦ 65k
0
gravatar for Alex Reynolds
3.0 years ago by
Alex Reynolds ♦ 28k
Seattle, WA USA
Alex Reynolds ♦ 28k 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 3.0 years ago • written 3.0 years ago by Alex Reynolds ♦ 28k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 818 users visited in the last hour