scAPP doc

folder

• scRNA: store all single cell RNA-seq data (10x platform), including scRNA-seq and snRNA-seq (from cellRanger)
• 10xATAC: store all 10x ATAC results (from cellRanger)

scripts

• RNA pbs: https://github.com/epigen-UCSD/epigen_ucsd_django/blob/master/utility/run10xCellRanger.pbs

• ATAC pbs: https://github.com/epigen-UCSD/utility_epigen/blob/master/run10xPipeline.pbs

• ATAC bash: https://github.com/epigen-UCSD/epigen_ucsd_django/blob/master/utility/run10xOnly.sh

• RNA bash: https://github.com/epigen-UCSD/epigen_ucsd_django/blob/master/utility/runCellRanger.sh

• updateSingleCellStatus.py: update singlecell object in database Usage: python updateSingleCellStatus.py -seqid SEQID -status STATUS where SEQID is the seq_id of a SeqInfo. A single cell object model must exist for this SeqInfo. STATUS is string of the status to update the database to e.g. "InQueue"