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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/wzthu/esATAC
Confirm the following by editing eac…
wzthu updated
7 years ago
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Hi,
Are there tests cases on the current implementation of sample-type (library)-specific Sample objects that extend Sample [as described in the docs](http://looper.readthedocs.io/en/latest/models.…
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Hi,
I have question regarding the nfrpos.bed output of nucleoatac.
In the help it is written "output_basename.nfrpos.bed.gz: NFR positions. Columns are (1) chrom, (2) left boundary (0-based), (3…
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Hello,
I am attempting to run your ATAC-Seq pipeline, just on some sample ENCODE data at the moment (thank you for sharing it!). I'm consistently running into an error at the IDR step that I'm not s…
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I tried running the search query URL and got the following error:
I ran
```
python ENCODE_downloader.py "https://www.encodeproject.org/search/?type=Experiment&assay_title=ATAC-seq&replicates.lib…
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Hello, I really like the atac-seq pipeline. I's very simple to use and powerful.
When I tried installing genome on my Linux environment using the command line below.
bash install_genome_data.sh…
ghost updated
7 years ago
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Hi kundajelab,
Thanks again for providing and updating the pipeline. I'm using the following version:
Latest git commit: 3f3eeefd9763a1e00ac81a2244cf17adac5c64a4 (Sun Feb 26 14:12:05 2017)
an…
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Here is one of the example:
/ifs/home/gongy05/.../ATAC-seq/pipeline/align-stats/results/align-stats.standard/align.by_sample.bowtie2/all-samples/alignment_barplots.pdf
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Hi Kai,
Congratulations on putting together a wonderful integration pipeline,i was testing this on one of our ms datasets and i encountered the following error.
[WARN][04-29 22:18] Link_TF_gene: F…
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Hi!
I am trying to run the pipeline and keep getting this error. I have tried:
export PYTHON_EGG_CACHE="/home/jet456/Pipeline/pythoneggcache"
chmod -R 777 /home/jet456/Pipeline/pythoneggcache
…