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Here's a strange question. I hope to have your guidance.
In the first genomic region I was interested in, I could successfully plot a perfect figure. However, when I select the second region of interest, there is a missing RNA-seq track in it, despite being able to run it properly. I have not set a max and min value and have repeatedly confirmed the presence of higher reads(values) in that region in the bw or bedgraph files (by loading file to IGV and manually extract specific region of interest). Other ChIP-seq tracks can be displayed normally. How do I fix this?
Another small question, why is the data range of IGV and pyGenomeTracks different for the same bw file? Is there a detailed documentation for the number_of_bins and summary_method parameters?
Hi,
Thanks for your bug report. I don't see any explanation for the missing RNA. I guess you already carefully checked the coordinates you are plotting. Would you mind to share with me one of the bw file?
Another small question, why is the data range of IGV and pyGenomeTracks different for the same bw file? Is there a detailed documentation for the number_of_bins and summary_method parameters?
The way pyGenomeTracks is working is with bigwigs:
Cut the plotting interval into number_of_bins equally sized intervals.
Compute a summary_method on each of this interval.
I think IGV is doing more or less the same except that you cannot control the number of intervals.
If you choose summary_method = max on both, you should have the same data range. If you choose summary_method = mean then it depends on the bin size and the bin boundaries...
Hi, @lldelisle
Here's a strange question. I hope to have your guidance.
In the first genomic region I was interested in, I could successfully plot a perfect figure. However, when I select the second region of interest, there is a missing RNA-seq track in it, despite being able to run it properly. I have not set a max and min value and have repeatedly confirmed the presence of higher reads(values) in that region in the
bw
orbedgraph
files (by loading file to IGV and manually extract specific region of interest). Other ChIP-seq tracks can be displayed normally. How do I fix this?Another small question, why is the data range of IGV and pyGenomeTracks different for the same bw file? Is there a detailed documentation for the number_of_bins and summary_method parameters?
I'm looking forward to your response!
Best,
Yao
test.png
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Partial configuration
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