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Say peppy offered a `project_modifiers.imply`, which is exactly the same as the `sample_modifiers` version but operates on a project. Then, I could do:
```yaml
name: global looper pipeline interfa…
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Hi!
I have been using the basenji_data.py script to recreate the tensorflow records used to train the basenji2/enformer model, after the tutorial in the preprocess.ipynb script. I tried three track…
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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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we should look at this...
| MGA repository: a curated data resource for ChIP-seq and other genome annotated data.
-- | --
| Dréos R, Ambrosini G, Groux R, Périer RC, Bucher P.
| Nucleic …
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Hi Jacob,
I'm using ChromBPnet to examine some ATAC-seq data, and I have a general question about preprocessing.
In the data processing section from the original ATAC-seq paper (Buenrostro et al…
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Credits to Katie Hoadley, who would be interested in using this on a dataset of hers
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run 01_generate_example_input_regions.py
Step 2: Load epigenomic data and store into arrays
DNase_seq
CTCF
Traceback (most recent call last):
File "01_generate_example_input_regions.py", …
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Hello,
When I run
```
gunzip -c chr*.fa.masked > hg19.fa
```
in [CENTIPEDE.tutorial](https://slowkow.github.io/CENTIPEDE.tutorial/) in Genomic sequence Section, I got the following error
…
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I read the CENTIPEDE manuscript. I think the author scanned all putative TFBS across the genome.
However, in your tutorial, you suggested using FIMO only to obtain TFBS in peak regions.
Is it pr…
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Hi,
Notably, I've previously installed the pipeline and it has worked fine.
This time the install_dependencies.sh step is failing to complete (see attached).
When I try to go ahead and run the pi…