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Przemol / seqplots

:chart_with_upwards_trend:SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
http://przemol.github.io/seqplots
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Issues with loading genome and .wig #34

Closed libri1 closed 6 years ago

libri1 commented 7 years ago

Hello, I met Julie at the CSH meeting recently and she told me about Seqplots - I just started using it and I have some issues. We would like to analyze strand specific RNA pol II data generated by the CRAC method, which generates (rather large) .wig files. I tried to add one of our tracks, using the option "custom" for the genome, but this did not work, and I got the following message:

image

Then I thought that this was due to not having the genome added, so I loaded SacCer3, but again it did not work and I got this message:

image

Still, my wig file contains the same numbering for the chromosomes, here is the beginning of the file:

image

It looks like the program has trouble converting the wig to bigwig and this relates to problems with the genome. As a final assay I tried to load our genome, we have it as a .genome package or fasta, but neither appeared as an available genome (the file appeared uploaded, but did not install). Any suggestion on how to solve these problems ?

Thank you very much Domenico Libri

Przemol commented 6 years ago

The conversion should work current version.

In rare case SeqPlots is unable to convert WIG to BW. If your conversion stil fails, please use "wigToBigWig" program from UCSC: https://www.encodeproject.org/software/wigtobigwig/

BW files are the default format for SeqPlots.