Comments (1)
Hi Murat,
I've fixed these issues and have additionally done a few things as we discussed recently: homogeneized stats reporting between ATAC- and ChIP-seq (including peak number reporting for ChIP); parameterization of bamToBigWig function - you can now control if you want to normalize your tracks or not in the pipeline config.
You can use either branch of pipelines or stick with open_pipelines, master branch. Maybe also make sure you have the latest dev from pypiper and looper <=v0.6-rc1 (the new v0.6-rc2 still has issues when working together with these pipelines).
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Related Issues (15)
- Add FASTQ input to all pipelines
- Add all required arguments as pipelines inputs HOT 2
- ATAC-seq pipeline exit if no mitochondrial reads are duplicated HOT 3
- Fastqc parser bug HOT 1
- set_file_path error HOT 10
- sambamba command not called as defined in the tools section of the atacseq.yaml pipeline file when generating oracle_FRiP using sambamba view
- Update to PEP stack 2.0 HOT 11
- bug here HOT 1
- Help needed with CROP-seq / open_pipeline isses
- Attribute reference to 'bigwig' on Sample in chipseq.py HOT 3
- Missing run_spp.R for chipseq.py HOT 3
- Peak count stat for SPP HOT 2
- Leveraging pypiper ngstk HOT 1
- Question: program naming for pipeline scripts
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