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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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For example, `rna_volume` is defined in nmdc-schema and associated with `Biosample`. We even have some tests for it.
If it is important to capture that information in the SubmissionPortal, so that …
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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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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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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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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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Andre, can you please summarize our email thread here regarding possible change to trimmer in the dnase pipeline?
Include the alternative packages, the criteria I outlined, and your answers to thos…
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I am using deeptools bamCoverage to analyze short (35-80bp) paired end fragments. All reads in my bam file are properly paired based on samtools flagstat and Picard. Yet bamCoverage extends some a…
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I tried the example json on the SCG cluster, and it exited with errors. I read in another issue that this type of error can occur if installed with mamba. However, I did not install with mamba. Please…
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Describe the bug
pipeline because javax.net.ssl.SSLException failed
OS/Platform
OS/Platform: [e.g. Ubuntu 18.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
Conda version: conda 22.9.0…