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Hi,
Thanks for developing such an excellent tool for single-cell genomics. I am wondering whether you could provide the processing pipeline for Easysci-ATAC-seq.
Thanks.
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Hello,
I am trying to run the pipeline for chicken samples and have tried to create a custom genome reference for the pipeline. However, after finishing the steps here [https://github.com/ENCODE-de…
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#11
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## **Invalid MEMLIMIT value with LSF on Linux**
When running the tutorial example for HPC with LSF, caper submits invalid memory unit format. Is lower case 'g' but should be 'G', resulting in the f…
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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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Hallo all,
I was reading the pepatac publication and I read a bit their pipeline. I find it to be the most interesting and comlete pipeline for ATAC.
Since it is very tough to get the whole pipeline…
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Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines:
https://github.com/kundajelab/atac-seq-pipeline
https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P…
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I was trying to build my own genome, but it never finished running and did not create the tsv file. I allocated 80G and run it overnight and still not finishes.
Below are files that have been gener…
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## **Describe the bug**
I tried to run this pipeline multiple times, and it kept getting stalled at task=atac.read_genome_tsv:-1. But there's no error message. It only stopped when timeout.
f1ce-4…