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and other basic parameters to determine quality of the run/ fastq file. The current log output for each alignment is not easy to understand.
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Hi,
Thanks for developing this user-friendly tool for ATAC-seq. I found some problems after running shiftGAlignmentsList, and the output BAM file is about half the size of the input file. I don't kno…
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I have noticed that insert sizes from BWA-MEM seem to start high at the beginning of a chromosome, and drop down towards the end. This isn't really an issue (feel free to close and ignore) but I wante…
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Hi,
I know this is an old error, but I have the same problem. I'm using ATACseqQC 1.8.5 and R 3.6.1, and I get the same error when I run more than one chromosome. It works with no problems for one ch…
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patent H3k36me3
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1. http://epigenomics.sdsc.edu:8088/Set_586/53f3be/setQC_report_chip.html
- H3K36me3 (`broadpeaks`): measuring gene body (RNA polymerase II (RNAPII) during transcription), def…
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Github actions for system testing [ran for ~0.5hr](https://github.com/uab-cgds-worthey/quac/actions/runs/5124929241), where we ran only one (WGS mode AND no prior QC data) of the [4 system tests](http…
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## Overview
A bug was found when using the default module for Snakemake on Biowulf (7.7.0). During the dry-run, it reports that additional rules (which weren't supposed to be running need to run). …
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Hi,
(in ATACseqQC 1.12.0)
the example of using plotCorrelation that is written in the ATACseqQC guide works out of the box only when asMates and bigFile parameters are FALSE in readBamFile. Otherwi…
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we need to define module-specific thresholds triggering potential warnings or errors.
pdp10 updated
6 years ago
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We use a python script to convert the "genome results" report from its original format to csv, which makes it easier to collect and compare metrics among multiple samples.
The original report forma…