The wig files

[Da-Peng Wang]

Dear Colleague,

I intend to convert BAM files to WIG files for UCSC genome browser as
we don't have webserver to store bigwig files at the moment.

Would you like to help me how to make the wig files that can be used in UCSC?

Thank you in advance,

Dapeng

[Hiram Clawson]

Good Morning Dapeng:

There are many procedures to construct such files from BAM files.
A google search for this procedure will find many such examples.

Here is another example, using the bedtools 'bamToBed' operation
and kent source commands:

bamToBed -i yourFile.bam | cut -f1-3 | sort -k1,1 -k2,2n \
bedItemOverlapCount -chromSize=yourGenome.chrom.sizes test stdin \
| sort -k1,1 -k2,2n > yourFile.bedGraph
bedGraphToBigWig yourFile.bedGraph yourGenome.chrom.sizes yourFile.bw

--Hiram

[Hiram Clawson]

Good Afternoon Da-Peng:

If your files are large, the upload is inefficient and will probably
not work. You can load tiny wiggle files, a few thousand data points
at most, but they are volatile and will disappear. I would recommend
finding a WEB hosting service where you can supply large files with
a URL. Please review your options for graphing data:
http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format
http://genome.ucsc.edu/goldenPath/help/bigWig.html
http://genome.ucsc.edu/goldenPath/help/wiggle.html

--Hiram

On 2/6/15 12:37 PM, Da-Peng Wang wrote:
> Hi Hiram,
>
> Thank you for your reply.
>
> But we don't have webserver to store bigwig files and
> "bedGraphToBigWig" is unable to generate the WIG file (not bigwig). We
> hope to upload the wig file to UCSC browser from PC.
>
> Could you please help me more?
>
> Thanks,
>
> Regards,
>
> Dapeng
>
> 2015-02-06 18:52 GMT, Hiram Clawson <hi...@soe.ucsc.edu>:

[Da-Peng Wang]

Hi Hiram,

Thank you for your reply.

But we don't have webserver to store bigwig files and
"bedGraphToBigWig" is unable to generate the WIG file (not bigwig). We
hope to upload the wig file to UCSC browser from PC.

Could you please help me more?

Thanks,

Regards,

Dapeng

2015-02-06 18:52 GMT, Hiram Clawson <hi...@soe.ucsc.edu>: