HiCUP

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Improve hicup2juicer

2

Dear HiCUP developers, I would like to add 2 options to the hicup2juicer converter: - `--digest` this would allow to retrieve the fragment id instead of the dummy values 0...

lldelisle

HiCUP output if Tidyverse, Plotly and/or Pandoc not installed

7

HiCUP does not give nice output if HTML summary reports are not generated owing to lack of Tidyverse, Plotly and/or Pandoc. Make this more elegant.

StevenWingett

HiCUP report di-tag size plot

2

Add calculated lengths to X-axis of size plot. Also set the starting zoom to something sensible.

StevenWingett

Truncation at very start of sequence.

1

Hi, Hope you're well. I just noticed this and wasn't sure if this was expected behaviour or not. It appears that when a ligation sequence appears at the very start...

StephenRicher

Assists with referencing for people using Scribler.

StevenWingett

Update documentation

4

StevenWingett

Bowtie2 Failing?

1

I suspect sometimes that Bowtie2 fails (e.g. exceeds RAM), but this is not caught by HiCUP. HiCUP proceeds and then generates error messages which appear to be a problem with...

StevenWingett

Integrate the capture script into main pipeline

1

Integrate capture script into main pipeline and print the results in the HiCUP summary report.

StevenWingett

The new HTML HiCUP summary report does not display percentages in the Mapping/Truncation graph. Add these.

StevenWingett

This shouldn't break anything and will mean that the code stands a chance of working on Macs which have a version of zcat which only works if the file name...

s-andrews