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output changes in differential MDS #4

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magruca opened this issue Jan 23, 2019 · 3 comments
Closed

output changes in differential MDS #4

magruca opened this issue Jan 23, 2019 · 3 comments
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@magruca
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magruca commented Jan 23, 2019

In GitLab by @magr0763 on Nov 7, 2018, 11:15

I have two suggested improvements for the differential MDS portion of DAStk, although the first could also be applied to the MDS calculation in process_atac

  1. It would be nice to have a specified output directory

  2. It would be helpful to have a .bed/.txt file (or really whatever tab/comma delimited file) that outputs the MDS and p-values for all motif calls between input conditions, significant or not, as well as the actual differential MD score displayed in the MD plot

@magruca
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magruca commented Jan 23, 2019

In GitLab by @magr0763 on Dec 21, 2018, 10:36

  1. It would be nice to not have to specify a prefix as it would be easier to integrate into the Nextflow pipeline. I understand the purpose of having the prefix, but for running all of the Nascent data, it would be easier to leave the SRR as the rootname

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magruca commented Jan 23, 2019

In GitLab by @igtr4848 on Jan 7, 2019, 12:34

assigned to @igtr4848

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magruca commented Feb 4, 2019

All changes made.

@magruca magruca closed this as completed Feb 4, 2019
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