Question: Any Method Of Converting Bigwig File Format Into Bed Format?
3
gravatar for samwise.techno
6.2 years ago by
samwise.techno30 wrote:

I want to have a bigwig file converted into gff after having the genome coordinates and genome annotation files converted from Hg19 to Hg18. One way, would be to convert bigwig into BED, use the liftover tool and then have the BED file converted into gff. Could someone please suggest a method to convert bigwig to BED, nothing available on the net.

bed bigwig • 21k views
ADD COMMENTlink modified 23 days ago by Samir160 • written 6.2 years ago by samwise.techno30

Hi there,

Any help on how to solve this error

./bigWigToWig input.bw output.wig udc couldn't read 4 bytes from input.bw, did read 0

Thanks in advance !

cheers CN

ADD REPLYlink written 6.0 years ago by Chirag Nepal2.2k

Clear the cache and check if the file is empty

rm -rf /tmp/udcCache

bigWigInfo​ file.bw
ADD REPLYlink written 3.8 years ago by Sukhdeep Singh9.8k
11
gravatar for Alex Reynolds
6.2 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

Instead of bigWigToBedGraph, you might use bigWigToWig, instead, as bedgraph is BED-like but isn't exactly BED, which may affect use of UCSC's liftover tool. In any case, both binaries are available from the UCSC executables download page.

Once you have the file in WIG format, you can convert it to a UCSC BED file with the BEDOPS wig2bed conversion utility.

Alternatively, you could take the bedgraph output and convert it to BED with an added GNU awk step:

$ awk '{ \
    if ($1 ~ /^chr/) { \
        print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; \
    } \
}' foo.bedgraph \
> foo.bed

You should be able to safely run it through liftover at that point.

ADD COMMENTlink modified 4.4 years ago • written 6.2 years ago by Alex Reynolds28k
2
gravatar for PoGibas
6.2 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

bigWigToBedGraph might be what you're looking for.

bedgraph format

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by PoGibas4.8k
0
gravatar for Samir
23 days ago by
Samir160
United States
Samir160 wrote:

Follow up to Alex's reply, here is an example:

wget http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw
## convert to intermediate wig format
bigWigToWig bigWigExample.bw out.wig
## convert wig to bed
wig2bed < out.wig > out.bed

bigWigToWig executable is from UCSC Kent utilities. Also, make sure to read manpage for wig2bed for details, particularly on 0- vs 1-based index and preserving header data.

ADD COMMENTlink modified 23 days ago • written 23 days ago by Samir160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1878 users visited in the last hour