Releases: CCBR/CHARLIE
Releases · CCBR/CHARLIE
v0.6
v0.5.5
- STAR2p output per gene counts and these per sample counts are aggregated into 3 count matrices:
- stranded
- unstranded
- reverse stranded
- config.yaml now includes 3 resource paths:
- original: hg38(masked) + rRNA + ERCC + legacy virus set from Mahesh
- v2: original + HSV1 strain 17
- v3: original + HSV1 KOS strain (with only 1 copy of repeats) --> this is now the new default
v0.5.4
v0.5.2
- Using picard to estimate duplicates using MarkDuplicates
- Generating a per-run multiqc HTML report
- Using eulerr R package to generate CIRI-CircExplorer circRNA Venn diagrams and include them in the mulitqc report
- Gather per job cluster metadata like queue time, run time, job state etc. Stats are compiled in HPC_summary file
- CLEAR pipeline quant.txt file is annotated for known circRNAs
v0.5.1
v.0.5.0
run_clear
is now set to True (as default)circ_quant
replacesclear_quant
in the CLEAR rule. In order words, we are reusing the STAR alignment file and the circExplorer2 output file for running CLEAR. No need to run HISAT2 and TopHat (fusion-search with Bowtie1). This is much quicker.