Copy the pipeline file sn-rna-seq-parsebio.smk, the scripts folder and the barcodes folder into the base directory of the sequencing run.
The script also expects
1. a folder starting with six digits (the date). Inside this folder should be the Sample Sheet (SampleSheet.csv) with relevant names and barcodes. For more information on what the Sample Sheet should look like, see XXX.
2. If basecalled already, add all .fastq.gz files into a folder called 01_basecalled.
Stuff about version control etc...
| kit | chem | nwells | bc1 | bc2 | bc3 | ktype |
|---|---|---|---|---|---|---|
| custom | NA | 1 | NA | NA | NA | special |
| WT_mini | v1 | 12 | n24_v4 | v1 | v1 | normal |
| WT_mini | v2 | 12 | n24_v4 | v1 | v1 | normal |
| WT | v1 | 48 | v2 | v1 | v1 | normal |
| WT | v2 | 48 | n96_v4 | v1 | v1 | normal |
| WT_mega | v1 | 96 | n192_v4 | v1 | v1 | normal |
| WT_mega | v2 | 96 | n192_v4 | v1 | v1 | normal |