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Call: `python bin/tf_analyzer.py -g mm9 -b liver`
Error:
```
76 of 152files were successfully normalised. If not all files were normalised, check logging for further information.
Traceback (mos…
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## Bi-weekly meeting memo
0. Files that Shannon will share to Tao
- ATAC-seq datasets: fastq
- variant dataset: vcf
- packages: R Bioconductor, ChIPPeakAnno, ChipSeerker
1. make the footprint f…
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Hi,
I would like some guidance as to where to find the .pwm files that the software requires. In the manuscript it states: "We obtained ChIP-seq and DNase-seq data from the ENCODE project and PWMs…
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I called the script with following parameters:
`python bin/tf_analyzer.py -g mm9 -b liver -t gata4 polr2a`
This called failed due to a connection lost to DeepBlue.
Because this downloads quite …
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To build the prediction model, you suggest thar we should have normalized and log2 transformed DNase-seq data and the log2 transformed and quantile normalized gene expression data. I don't have DNase…
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Hello,
I am using MAESTRO docker image winterdongqing/maestro, 1.2.1, 57f41ffbe200. When I ran the scRNA-seq module, it reported errors like:
`unable to open file: name = '/project/dev/qqin/LI…
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Hi,
first thanks for the tools, and the tutorial!
I am having troubles with a couple of DNAse-seq BAM files (here an example: https://www.encodeproject.org/experiments/ENCSR136DNA/)
Catchitt th…
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Hi, I am trying use lisa to my own ATAC samples. Now I have a N*m matrix and a input gene list, which N represent N ATAC peak region and M reprsent M samples.
I am wordeing whether I can apply lisa …
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submission sheet: https://docs.google.com/spreadsheets/d/1eeFWWwAGgtrrfiWj46GZQcT3bfZMYZGg/edit#gid=58955629
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## **Describe the problem**
When running the encode chip-seq-pipeline on HPC with SLURM, it consistently hangs on the line that reads "task=chip.read_genome_tsv:-1, retry=0, status=WaitingForReturn…