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running the code Pebblecounts.py, after the selection of filters, in scale 1 of 3 a large number of windows are tested:
How can I set manually the window size (or the windows number)??
```
..…
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### Description
When attempting to access the settings of the `tophat` extension, an error is thrown related to the Gnome Shell's Clutter library. It seems that the typelib file for Clutter is not fo…
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I recently came across this library when looking for a fast GPU implementation of a white top-hat transform (`result = data - dilate(erode(data))`) with python bindings. The only thing I found was th…
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![tophat-temp-issue](https://github.com/fflewddur/tophat/assets/4774314/0a724bbb-8c30-4070-aede-5b7236b76c3e)
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Hi,
Im preatty new in the field of bioinfomatics, and I having some issues runing the program. We used TopHat Aligner to create some bam files (I used the --MinMAPQ 50, because it was recomended). I…
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Hi,
In the mapping with tophat-fusion step, I get the below error:
```
$ clear_quant -1 206_1.fq.gz -2 206_2.fq.gz -g /library/hg19.fa -i /library/hg19.fa -j /library/hg19.fa -G /library/hg19.g…
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I have installed all the bowtie, tophat and samtool packages recommended for the tophatfusion run, but getting this error, it cant locate my samtools. I have version you have asked to install...Kindly…
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## Description
Hello Christopher, we sure would like a fancy goots wearing a tophat and/or a monocle.
![image](https://github.com/christrotter/gootsmoji/assets/12434761/0ee8e5c9-0c26-48f8-9428-9…
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Hi,
I want to annotate tophat fusions.out file with gene names. So after running Tophat with --fusion-search option, I got fusions.out file. Now I want to run tophat-fusion-post. I have cretaed the r…
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The code seems to assume a Gaussian beam profile, I would like to simulate a MOT geometry using laser beams with a tophat profile or more generally be able to modify the beam profile to be an abritrar…