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I am trying to run the example JSON using singularity and the job keeps getting stuck without a clear error message. This is the command I'm running:
```
echo "source /broad/software/scripts/useus…
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Hi !
I am trying tu use msCENTIPEDE to generate TF footprints for several ATAC-seq data sets i've produced.
I wanted to have general advices on how to achieve the most accurate workflow.
So far, w…
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## **Describe the bug**
I am trying to install the atac-seq-pipeline and having issues with installing the conda environments to even get the pipeline installed. Have been trying this for few weeks n…
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Hi,
another problem with phantompeakqual or with R
```
Decompressing ChIP file
Decompressing control file
Loading required package: caTools
Reading ChIP tagAlign/BAM file Hs_940_temp//M940_…
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Hi all,
Thanks for this great tool! I have a question on its use though.
Could the user examine the binding specificity of the motifs in your models by querying a sequence > 10000b introducing an …
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Cross-posting this issue from nboley/idr repository, as I think the issue using IDR is related to the output from MACS2 call peak:
Trying to call peaks on an ATAC-seq sample (using the ENCODE ATAC-…
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Ciao! Thanks for joining this project!
I am Luca Pinello the team leader for @hackseq/2016_team_4 .
I am currently an Instructor at Dana-Farber Cancer Institute/Harvard School of Public Health and …
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A "as simple as possible" init script usable for each DEEP pipeline that identifies itself (WGBS, ChIP-seq etc.) and loads - if necessary - required reference data/configurations from the reference re…
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I stumbled on your software, and would be interested to use it on an HPC cluster (e.g., with job management via SLURM). Do you have documentation / protocol to do this? Is running the server (with the…
vsoch updated
5 years ago
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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 …