uploading bigWig files for reverse strand

[dahun73]

Hello,

Thank you for serving such a nice tool in advance.

I tried to upload bigwig files that were separated for forward and reverse strand. In case of reverse stranded bigWig files, they have negative values to visualize opposite direction.

The workflow to make these reverse stranded bigWig files is:

1. First, I used 'bamCoverage' in 'deeptools' to make bigWig files(they have positive values in this time).
2. I converted bigWig files to bedGraph and added minus to 4th column.
3. Finally, I converted bedGraph files to bigWig files again.

So, I uploaded those bigWig files.

The first file is forward stranded bigWig file. It was well uploaded. However, reverse stranded bigWig file was not(the second file). I adjusted y axis value and it was not working. Are there any problems to make bigwig files or adjust parameters?

Thank you in advance

[lidaof]

Hi @dahun73 a quick solution without any of my effort is you can use your bedgraph file with both positive and negative values, don't make it to bigwig, but bgzip and tabix -p bed to index it, then use it as a bedgraph track.

I would need the bigwig file url to take a look, you can DM me please :)