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Is there a way to run PePr without specifying input files, as is the case for analyzing ATAC-seq/DNase-seq data?
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Hi,
Could you maybe add an explanation of what exactly the ATACseq mode (-A flag) is doing differently to DNase mode? Also should the input BAMs for ATACseq mode be Tn5 shifted or not?
Thanks
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## **Describe the bug**
Running the example on the README (`caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name ANY_GOOD_LEADER_JOB_NAME`) submits leader job to LSF, but imme…
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## Line 46 of [ATAC-seq/auyar_scripts.sh](https://github.com/TheJacksonLaboratory/ATAC-seq/blob/master/auyar_scripts.sh):
`echo python $scriptDIR/auyar/pyadapter_trim.py -a $outputDIR/trimmomatic/\$F…
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T cell subsets are likely best distinguished w/ ATAC-seq data so we should track down some.
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IWC already contains a sufficient number of workflows that can be readily used for BRC purposes. We need to understands:
- understand which categories of workflows we have
- based on these categories…
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Hi,
I have seen most papers doing ATAC-Seq analysis run macs2 with the --nolambda option, including the hmmratac paper. Naively, it seems like this would overcall peaks/peak summits in generally op…
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The main challenge with using this pipeline for ATAC-seq data is the use of STAR for mapping within the WASP subworkflow. We could create two new mapping rules within the WASP subworkflow that use `bo…
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Determine how fragments files will be linked to a dataset. A user should be able to easily determine if a dataset has fragments and retrieve them from the API.
## DoD
An outline of work that descr…
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Hello,
I'm interested in using scglue to integrate my scRNAseq with scATACseq data, comprising four paired samples. These datasets are not multiome; they're only paired samples.
After processing…