Wigtobigwig: What'S Wrong With My Wig File ?

Question

[Pierre Lindenbaum]

I've generated a wig file for the chr22. The data is a sliding window (window-size=500, every 250pb) starting from pos0=16050276. The windows overlap over 250pb.

$ head input.wig
fixedStep chrom=chr22 start=16050276 step=250 span=500
4
3
5
5
2
3
3
2
3

there is only one header in my file:

$ grep -i -c Step input.wig 
1

and there is 140777 lines (including the header)

$ wc -l input.wig 
140777 input.wig

length(chr22)=51304566

$ grep chr22 sizes.tsv 
chr22    51304566

but when I want to convert my wig to a bigwig file using wigToBigWig, I get the following error:

wigToBigWig input.wig sizes.tsv out.bw
There's more than one value for chr22 base 16306276 (in coordinates that start with 1).

I must be very tired, do you know where is my error ?

[Sukhi Singh]

Check this post, similar might help you!!

[Pierre Lindenbaum]

@Sukhdeep so, the wig format doesn't handle the overlapping/sliding windows ?

[Sukhi Singh]

I dont work with wiggle files (variable & fixed), I use bedgraph format, which I think is more comprehensible and easy to work with. In the end, I convert bedGraphs to bigwig, which is for sure better, in terms of sample management, load on server plus less size.

[Damian Kao]

don't you need 2 columns for wig files? first column is the base position and second column is the count. *edit. nevermind its fixedstep.

[Chris Miller]

Do you have more than one value on a line somewhere? Specifically, check around line 1024: (16306276−16050276)/250 = 1024

or just awk '{print $2}' input.wig | sort | uniq

[varsha619]

Hi I am trying to run -

grep -hv 'track' *.wig | wigToBigWig -clip stdin chrom.sizes out.bigwig

Could you please let me know how you fixed the error - There's more than one value for chr2? Thank you.