Errors with sort-bed

Question

[catherine]

I have bigwig file downloaded from GEO, and convert it to wig file using bigwigToWig (ftp://hgdownload.cse.ucsc.edu/apache/htdocs-rr/goldenPath/help/bigWig.html). And when I want to used sort-bed command in BEDOPS, it gives me error like this:

Non-numeric start coordinate. See line 1025 in GSM723005_H3K4me1-MEF.wig.

​But I checked manually and didn't find anything wrong in this file.

If I don't use sort-bed, but just use convert it to bed file by myself, then run BEDOPS, it returns me empty output file (although I think the file is already sorted).

Any idea what went wrong to my procedure?

Thank you very much!​

[Manvendra Singh]

First, convert your wig file into bed. I would suggest to use wig2bed from bedops.

Then run sort-bed command on your converted file

[catherine]

yeah! i got it. tHANK YOU

[Pierre Lindenbaum]

are you trying to sort a WIG file with a sort-BED tool ??

[catherine]

yeah, Im trying to use sort-bed in BEDOPS, it is said the input could be wig file.

[Manvendra Singh]

No, It does not say that.

It says that

The sort-bed utility requires one or more three-column BED file(s). Support for common headers (such as UCSC BED track headers) is included, although headers will be stripped from the output

[catherine]

Sorting arbitrarily large BED files is easy with sort-bed, which easily scales beyond available system memory, as needed. We also offer portable conversion scripts that transform data in common genomic formats (SAM/BAM, GFF/GTF, PSL, WIG, and VCF) to sorted BED data that are ready to use with core BEDOPS utilities.

http://bedops.readthedocs.org/en/latest/content/overview.html#bedops-tools-are-flexible

It's misleading

Answer 1

[Alex Reynolds]

Sounds like you need to do something like:

$ wig2bed < GSM723005_H3K4me1-MEF.wig > GSM723005_H3K4me1-MEF.wig.bed

Like most BEDOPS apps, the wig2bed application exports sorted data by default, so you shouldn't need to pipe to sort-bed.

You would need to sort if you explicitly set wig2bed not to sort, as in the following:

$ wig2bed --do-not-sort < GSM723005_H3K4me1-MEF.wig | sort-bed - > GSM723005_H3K4me1-MEF.wig.bed

See wig2bed --help for a description and listing of options.