sciATAC

For nextseq runs:

demultiplex

The procedure is the same as other nextSeq runs, but:

• Enter runInfo: S2
• The i7index and i5index in this context will be the plate number. Each plate contains 96 barcodes as a unit. So if enter i7index: 1, it means barcodes from 1-96; if enter i5index:1,2,3,4,5,6,7,8, it means barcodes from 1-768;
• it is calling ./utility/runDemuxSnATAC.sh which passes run_dir and flowcell_id to runDemuxSnATAC.pbs@tscc.

Sequencing_ID i7index i5index lane(separated by Space or Tab)
MM_419 1 1,2,3,4,5,6,7,8
MM_420 2 1,2,3,4,5,6,7,8
**Not found in metadata app: MM_419,MM_420. Please add them in metadata app first.**

Example seqRun in LIMS: http://epigenomics.sdsc.edu:8000/nextseq/236/ (search S2)

cooladmin pipeline

• run through ./utility/coolAdmin.sh to submit job to tscc and call /projects/ps-epigen/software/snATACCoolAdmin_LIMS/10x_model.bash