processing pipeline for ENCODE multiome datasets and GEO datasets (no fragment file available, FASTQ only)
datasets used for REMO performance analysis:
- bile duct
- fallopian tube
- heart
- left colon
- liver
- lung
- muscle
- pancreas
- placenta
datasets used for REMO annotation:
- pancreas1
- pancreas2
- pancreas3
- pancreas4
- retina1
- retina2
- retina3
- retina4
- retina5
- retina6
- retina7
- retina8
dataset ID and FASTQ download SRA/link can be found in datasets.csv
software versions:
- Cellranger-ARC 2.0.2
- Reference version: 2020-A, Human GRCh38 (GENCODE v32/Ensembl98)
the provided ENCODE gex matrix contained decimals when it should just be integers, this pipeline downloads the FASTQ files and re-processes them using cellranger-arc
part of REMO project