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Hi @leepc12 , first, thank you for the great pipeline here 🙏
## **Describe the bug**
The failure is partially due to my input fastqs having identical file name and differs as different file on pa…
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Hi,
I have a problem running the command 'scTEATAC': When runnning
`scTEATAC -i input.bam -o outfile -x mm10.te.atac.idx` I receive the error
> scTE_scatacseq: error: the following arguments …
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Hello there,
I'm trying to use scDesign3 to simulate single-cell ATAC-seq data, and I like your cool results shown in FigureS6 and S7 of the paper. But so far I cannot repeat that on another datase…
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On scg, I'm running
module load caper
module load java
caper run atac.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json
…
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Does the pipeline apply the standard +4/-5 offsets to aligned reads to account for the precise Tn5 binding site? I have not been able to find this in the documentation or in the code base.
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Hi Jin,
I recently run ENCODE pipeline and run an error "MarkDuplicates" of picard. Based on the stderr file:
File "/home/yanyang8/ll/envs/encode-atac-seq-pipeline/bin/encode_task_filter.py", …
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## **Describe the bug**
What I ran:
(base) [azstephe@compute-1-13 atac-seq-pipeline]$ caper run atac.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR…
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I have checked the format of the ATAC.se and the RNAmat.They are SummarizedExperiment and matrix. But when I ran runGenePeakcorr, I still have this problem.
```
cisCorr
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Exception thrown on pipeline launch, seems to be a Caper problem (get same output when running caper without input JSON). Running on SLURM cluster with pipeline v1.8.0.
**Caper configuration file**…
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Hello,
I'm very new to machine learning and wanting to run Baskerville (as suggested by @davek44 on the Basenji page).
I was wondering if you had any beginner-friendly guidance for how to imple…