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## **Describe the bug**
When running the newest pipeline (v2.2.0) with TEST command `caper run chip.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR00…
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there was a pretty significant change made to the code in the past 2 months which got haplocheck working properly, not sure what that was but thank you for that.
I wanted to drop some notes here b…
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_(Using notes from @andrerom to try to create an overall epic for v2 requirements)_
# v2 Revamp Requirements Epic
## Scope
This Epic defines requirements and approaches for further activities mov…
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### Description
When trying to process sct_run_batch following instructions on sct website, it works, but only for for the sample data. When those instructions are applied to a "real world" dataset…
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### Contact Details
_No response_
### Description of changes
[workbook (15) (1).xlsx](https://github.com/ranchobiosciences/Data_Modeling_Issues_Templates/files/10815512/workbook.15.1.xlsx)
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The output should contain the following files.
1. phenomized JSON files in data/PEDIA/jsons/phenomized
2. Each file which passed QC should has a VCF file in data/PEDIA/mutations. The VCF is converte…
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To connect the PASS1B-06 DEA results data to the phenotypic data, we need to map each unique `feature_id` (present in the DEA results) to a list of associated `vial_label` (present in the phenotypic d…
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Tests show removing secondary alignments by default leads to much closer read numbers to original fastq compositon, when using simulated data.
Seems to be specific to minimap2 and esp long reads.
…
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# OHW23 Projects
[List of all projects from OHW23](https://oceanhackweek.org/ohw23/projects/projects_thisyear.html)
I'm going to pick one or two projects from OHW23 to start with.
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Hi,
I was wondering if adding the feature of shifting and splitting the reads after the alignment would be helpful.
A recent review on the approaches to analyze ATAC-seq data ([Yan et al., 2020]…