Bedgraph To Wig

Question

[alive]

How to convert bedgraph to wig ? I tried converting bedgraph to bigwig and bigwig to wig using the kent tools. But no luck!

input looks like this

chr19 59302000 59302300 -1.0
chr19 59302300 59302600 -0.75
chr19 59302600 59302900 -0.50
chr19 59302900 59303200 -0.25
chr19 59303200 59303500 0.0
chr19 59303500 59303800 0.25
chr19 59303800 59304100 0.50
chr19 59304100 59304400 0.75
chr19 59304400 59304700 1.00

Answer 1

[dli]

What error messages does bedGraphToBigWig claim?

Do you use the right chrom.sizes file?

Please also notice that bedGraphToBigWig require a sorted input file

$ bedGraphToBigWig 

bedGraphToBigWig v 4 - Convert a bedGraph program to bigWig.

usage:
   bedGraphToBigWig in.bedGraph chrom.sizes out.bw

where in.bedGraph is a four column file in the format:
 <chrom> <start> <end> <value>

and chrom.sizes is two column:  
 <chromosome_name> <size_in_bases>

and out.bw is the output indexed big wig file.

The input bedGraph file must be sorted, use the unix sort command:
  sort -k1,1 -k2,2 unsorted.bedGraph > sorted.bedGraph

options:

   -blockSize=N - Number of items to bundle in r-tree.  Default 256
   -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
   -unc - If set, do not use compression.

[Shicheng Guo]

1. bedGraph has a header: track type="bedGraph" description="***", I think you can not sort directly with

   sort -k1,1 -k2,2 unsorted.bedGraph > sorted.bedGraph
   

2. Be sure your bedGraph only has 4 columns.

Answer 2

[Alastair Kerr]

They are already a very similar format. Indeed the wigToBigWig program in the kent package can use a bedgraph format as input.

Note there are many different type of wig format. (Variable step etc). So it depends what you are looking for.

• Some wig files (aka wigbed) start conting from 0, others from 1. Bed (and bedgraph) usually starts from 0.
• bedgraph is usually tab separated, whereas wig is space separated.

Therefore the simplest way to convert bg to wig:

1. Optional: you may need to subtract 1 from each number in the bedgraph and convert tabs to spaces
   • perl -ne '@a = split; $a[1]--; $a[2]--; join (" ", @a)' infile > outfile
2. Add a track line to the top of the file
   • track type=wiggle_0 name=\"COMBINED\" description=FILENAME"
3. Convert tabs to spaces ( alternative to step one)
   • tr '\t' ' ' < infile > outfile

[alive]

I would like it to be in variable step wiggle format.

Answer 3

[Sukhi Singh]

Please give the error messages, I have experienced 5 different kinds of errors while doing this conversion and each error is linked to a different solution. Also, check this tutorial for bigWig conversion and viewing. Also, if bedgraph file is big, you should stick to bigBed or bigWig.

Cheers