Snakemake_ATAC_2020 issueshttps://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues2021-02-24T16:54:54+01:00https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/5Add MultiQC 2021-02-24T16:54:54+01:00ChouarefAdd MultiQC *Created by: JihedC*
https://github.com/ewels/MultiQC*Created by: JihedC*
https://github.com/ewels/MultiQChttps://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/2Add parameters of deeptools to the configuration file2021-03-17T13:59:10+01:00ChouarefAdd parameters of deeptools to the configuration file*Created by: JihedC*
Deeptools has a lot of arguments, such as the bin size or the smoothlength.
All argument need to be included in the configuration file so that we can modify the parameters easily *Created by: JihedC*
Deeptools has a lot of arguments, such as the bin size or the smoothlength.
All argument need to be included in the configuration file so that we can modify the parameters easily https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/11Pipeline not working on dev branch2021-03-19T11:36:25+01:00ChouarefPipeline not working on dev branch*Created by: JihedC*
Hi Jianhui,
I was trying to run the pipeline on shark but I have got this error message:
'''
Start time : Wed Mar 17 14:35:21 CET 2021
/exports/humgen/jihed/miniconda3/lib/python3.6/site-packages/snakemake/wor...*Created by: JihedC*
Hi Jianhui,
I was trying to run the pipeline on shark but I have got this error message:
'''
Start time : Wed Mar 17 14:35:21 CET 2021
/exports/humgen/jihed/miniconda3/lib/python3.6/site-packages/snakemake/workflow.py:26: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
from snakemake.parser import parse
Building DAG of jobs...
Creating conda environment envs/homer.yaml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /exports/humgen/jihed/Jianhui/Snakemake_ATAC_2020/ATAC-seq_pipeline/rules/../envs/homer.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
ResolvePackageNotFound:
- hmmratac=4.11
End time : Wed Mar 17 14:35:39 CET 2021
'''
I think there is a mistake with the version of hmmratac. On conda I can find only hmmratac 1.2.10.
Can you fix this please?https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/4Coverage over other bed files2020-12-28T12:11:30+01:00ChouarefCoverage over other bed files*Created by: JihedC*
For now the pipeline uses the gencode bedfile to measure chromatin accessibility around the gene body.
We want to include other bedfiles, such as protein binding sites or repeat.
*Created by: JihedC*
For now the pipeline uses the gencode bedfile to measure chromatin accessibility around the gene body.
We want to include other bedfiles, such as protein binding sites or repeat.
https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/8HMMRATAC is not downloaded by the pipeline2021-01-04T17:28:30+01:00ChouarefHMMRATAC is not downloaded by the pipeline*Created by: JihedC*
Now HMMRATAC works but the tool is not downloaded by the pipeline.
We can either add a rule to download it from GitHub (also include a touch command) or try to use the conda version of HMMRATAC.
First try conda...*Created by: JihedC*
Now HMMRATAC works but the tool is not downloaded by the pipeline.
We can either add a rule to download it from GitHub (also include a touch command) or try to use the conda version of HMMRATAC.
First try conda, it's the simplest.https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/1Include more Deeptools tool2021-03-17T14:01:47+01:00ChouarefInclude more Deeptools tool*Created by: JihedC*
For the pipeline we also want to include the following tools:
- [bamPEFragmentSize](https://deeptools.readthedocs.io/en/develop/content/tools/bamPEFragmentSize.html)
- [plotCorrelation](https://deeptools.readth...*Created by: JihedC*
For the pipeline we also want to include the following tools:
- [bamPEFragmentSize](https://deeptools.readthedocs.io/en/develop/content/tools/bamPEFragmentSize.html)
- [plotCorrelation](https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html)
- [plotProfile](https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html)
https://git.lumc.nl/jchouaref/Snakemake_ATAC_2020/-/issues/6Add annotation of the peaks with Homer 2021-03-19T15:33:23+01:00ChouarefAdd annotation of the peaks with Homer *Created by: JihedC*
Homer can be used to annotate the peaks detected by ATAC-seq. This will give us information about the genomic feature associated with the peak.
Information about peak annotation: http://homer.ucsd.edu/homer/ngs/a...*Created by: JihedC*
Homer can be used to annotate the peaks detected by ATAC-seq. This will give us information about the genomic feature associated with the peak.
Information about peak annotation: http://homer.ucsd.edu/homer/ngs/annotation.html
Homer can be installed with Conda: https://anaconda.org/bioconda/homer