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Hi,
I have been trying to run your pipeline on the mm10 data set (as setup by running install_genome_data.sh ). As there were no fast files, I made a bam file from the bed files and am running the…
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I think there are issues with the download button for upset plots? I get this error:
```
--- Running overlap_upset_plot() ---
overlap_upset_plot(): Done in 40.8s.
Quitting from lines 338-351 (Ep…
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- **acted_on_behalf_of**
- **ended_at_time**
- **has_maximum_numeric_value**
- **has_minimum_numeric_value**
- **has_numeric_value**
- **has_raw_value**
- **has_unit**
- **latitude**
- **longi…
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Hi,
I am trying to use msCentipede on a ATAC-seq time course series without success. I get an error when running a command like
python call_binding.py --task learn --protocol ATAC_seq testbk/Ctcf_…
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Hello,
Thanks for your contribution to develop this tool. Could you give me any hints about how to use FLAMINGO to construct 3D organization in specific region? Like 1-2Mb ? And I urgently need thi…
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Credits to Katie Hoadley, who would be interested in using this on a dataset of hers
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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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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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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…
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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…