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Review MultiQC Custom Content in Main Table #90
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@apeltzer looking awesome so far! Things that I think would be great are:
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Not so much a metric, but have 'number of reads after quality filtering' column, when that flag is initiated. |
To summarize a bit what Phil said, I guess we'll need a custom plugin for MultiQC to provide some of these here. So we should create a list of required metrics and how to compute them and have these available then. |
For reference, this are some of the typical EAGER 1 headers. I will update definitions (as I understand them) over the next couple of days.
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Additional stuff from EAGER1 modules which wasn't in original ReportTable
Additional stuff which has been added to EAGER2 already
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I can potentially supply an R/tidyverse script that converts a MultiQC Json to a nice table however a couple of things to note:
Point two references: |
Extra values for the polyG to consider is effect on GC content, but we need to decide how to display this (i.e. which modules to get this info from). |
MultiQC ReportTable RequestsIn all cases: either Adapter Removal
Samtools
Qualimap
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Need to update this according to requirements we have - there have been a lot of updates on this one recently, e.g. supprt for mtnucratio in MultiQC, mean coverage updates in MultiQC using QualiMap. |
Most needed stuff is there, but no endogenous DNA. Maybe a small python script required and a MultiQC module? @aidaanva would you be interested? It would just need to take a single samtools flagstat file and divide the mapped field (5th row) by the total (1st) and spit out a percent. |
I can do it |
Your script could actually run in the |
Endogenous DNA added. Will close for for 2.1, but can reopen in the future for next MultiQC Release |
I'd like to have a better and improved report in the end, summarizing certain important metrics in a smart way, e.g. but not limited to. Naming is something I'd not like to standardize too much since different labs tend to have different names for certain metrics.
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Could you please add things that are of specific interest to you?
These here are on my ToDo list:
Schmutzi / estimates for contamination
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Any ideas what you'd like to see here @EisenRa @jfy133 @JudithNeukamm ?
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