diff --git a/docs/usage.md b/docs/usage.md index e5682b07..73f6766f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -266,14 +266,62 @@ Cellranger multi needs a reference for GEX and VDJ analysis. They are calculated Cellranger multi also requires some additional data/information when utilizing some specific Feature Barcode Technologies: -TODO: talk about these: -gex_frna_probe_set = null +**FFPE and CMO barcodes** +You must provide those via a CSV with the `--cellranger_multi_barcodes` parameter. The file should look like this: + +```csv +sample,multiplexed_sample_id,probe_barcode_ids,cmo_ids,description +PBMC_10K_CMO,PBMC_10K_CMO_PBMCs_human_1,,CMO301,PBMCs_human_1 +PBMC_10K_CMO,PBMC_10K_CMO_PBMCs_human_2,,CMO302,PBMCs_human_2 +4PLEX_HUMAN,Liver_BC1,BC001,,Healthy liver dissociated using the Miltenyi FFPE Tissue Dissociation Kit +4PLEX_HUMAN,Ovarian_BC2,BC002,,Ovarian cancer dissociated using the Miltenyi FFPE Dissociation Kit +4PLEX_HUMAN,Colorectal_BC3,BC003,,Colorectal cancer dissociated using the Miltenyi FFPE Dissociation Kit +4PLEX_HUMAN,Pancreas_BC4,BC004,,Healthy pancreas dissociated using the Miltenyi FFPE Tissue Dissociation Kit +``` + +TODO: Complete the ones below. Do not have a real understanding. + +The set of CMO reference sequences with `--gex_cmo_set`. + +The frna probe reference sequences with `--gex_frna_probe_set`. Example: + +```csv +#probe_set_file_format=2.0 +#panel_name=Chromium Human Transcriptome Probe Set v1.0.1 +#panel_type=predesigned +#reference_genome=gex_reference +#reference_version=2020-A +gene_id,probe_seq,probe_id,included,region +ENSG00000000003,GGTGACACCACAACAATGCAACGTATTTTGGATCTTGTCTACTGCATGGC,ENSG00000000003|TSPAN6|8eab823,TRUE,spliced +ENSG00000000003,TCTGCATCTCTCTGTGGAGTACAATCTTCAAGTTTACAGCAACTCTTAGG,ENSG00000000003|TSPAN6|9d7fe51,TRUE,unspliced +ENSG00000000003,AAAGCTGTTCTTAATCTCATGTCTGAAAACAAATCCTACGATGGCAGCGA,ENSG00000000003|TSPAN6|d2b5833,TRUE,spliced +[...] +``` + +**Feature barcode reference for antibody capture** + +File containing feature barcodes used for AB analysis (`--fb_reference`). Example: + +```csv +id,name,read,pattern,sequence,feature_type +CD3,CD3,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTCATTGTAACTCCT,Antibody Capture +CD4,CD4,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGTTCCCGCTCAACT,Antibody Capture +CD8,CD8,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCGCAACTTGATGAT,Antibody Capture +CD11c,CD11c,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TACGCCTATAACTTG,Antibody Capture +CD14,CD14,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCTCAGACCTCCGTA,Antibody Capture +CD16,CD16,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AAGTTCACTCTTTGC,Antibody Capture +CD19,CD19,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTGGGCAATTACTCG,Antibody Capture +CD56,CD56,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCCTTTCCTGATAGG,Antibody Capture +CD45,CD45,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCCCTTGCGATTTAC,Antibody Capture +IgG1,IgG1_control_TotalSeqC,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCCGGACGACATTAA,Antibody Capture +A0201_NLVPMVATV_CMV_TCR-1,NLVPMVATV_CMV_TCR-1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GGCCTCGGTCCTAGG,Antibody Capture +``` + gex_target_panel = null -gex_cmo_set = null -fb_reference = null vdj_inner_enrichment_primers = null gex_barcode_sample_assignment = null -cellranger_multi_barcodes = null + +TODO: ends here ## Running the pipeline