Closed
Milestone
1.0.0
Milestone ID: 21
Update pipeline to start with fastqs
Unstarted Issues (open and unassigned)
0
Ongoing Issues (open and assigned)
0
Completed Issues (closed)
27
- Missing modules
- Fix software versions test
- Update Astrocyte documentation and errors
- Fix astrocyte run
- Fix tests for software versions
- New folders for all steps
- skip motif search and diff bind
- Last 3 steps don't go into user defined output directory
- Add Pearson correlation, and make Spearman and Pearson Corr Plots pdf
- experimentQC plots are empty in PE
- Test Astrocyte
- Use SampleIds/ Experiment Id as file names throughtout pipeline
- Add defined output folder
- Output software versions and methods and references
- Add multiqc summary of data
- broken link in documentation
- Add in current chip-analysis functionality.
- Pool and Pseudoreplication
- Make tagAlign files
- Remove qc_fastq.py
- Add in grouping variable
- Update documentation
- Add in Macs2 support
- Update deeptools
- Include Phantompeakqualtools step
- Bam Stats and Filter
- Add mapping and trimming
