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Hi there,
I have a problem running the pipeline which I have set up on a SLURM HPC. It had worked previously and I used it regularly for the best part of a year. However it stopped working after a …
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I have a workflow question. Here is some background:
I have a Seurat RDS file of integrated ATAC-seq and RNA-seq data from human samples. This data measures TF expression. After running PCA and UMA…
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Hi,
I send a job with the command:
bds /nethome/fxf201/bin/encode_atac_update/atac_dnase_pipelines/atac.bds -species hg19 no_par -out_dir sh11_cy_ctrl -enable_idr -multimapping 4 -smooth_win 73 -a…
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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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## **Describe the bug**
When running the newest pipeline (v2.2.0) with TEST command `caper run chip.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR00…
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Hi Huamei,
I'm trying to predict cell proportions with your tools for ATAC-seq data and it does not work even I'm running the example data.
The command with issue is "deconPeaker.py deconvolution…
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Excellent work! I noticed that in your tutorial available at [https://slat.readthedocs.io/en/latest/tutorials/basic_usage.html], you provided two preprocessed datasets. Could you please provide additi…
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## **Describe the bug**
caper.cromwell.WomtoolValidationFailed: RC=1
## **OS/Platform**
- OS/Platform: [e.g. Ubuntu 18.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
- Conda version: 4.13…
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Thank you for providing very useful software.
I wonder if this software is suitable for bulk tissue ATAC-seq and RNA-seq.