Package: fba
工欲善其事，必先利其器。—— 论语·卫灵公fbaTools for single-cell feature barcoding analysisJialei Duan, Gary C Hon,FBA: feature barcoding analysis for single cell RNA-Seq,Bioinformatics, Volume 37, Issue 22, 15 November 2021, Pages 4266–4268. DOI:https://doi.org/10.1093/bioinformatics/btab375. PMID:33999185.What isfba?fbais a flexible and streamlined toolbox for quality control, quantification, demultiplexing of various feature barcoding assays. It can be applied to customized feature barcoding specifications, including different CRISPR constructs or targeted enriched transcripts.fbaallows users to customize a wide range of parameters for the quantification and demultiplexing process.fbaalso has a user-friendly quality control module, which is helpful in troubleshooting feature barcoding experiments.Installationfbacan be installed withpip:pipinstallfbaAlternatively, you can install this package withconda:condainstall-cbiocondafbaWorkflow ExampleCRISPR screening10k A375 Cells Transduced with (1) Non-Target and (1) Target sgRNA, Dual IndexedCROP-seq; 1:1:1 Mixture of DNMT3B, MBD1, and TET2 Knockout Cell Lines (HEK293T)Direct-capture Perturb-seq; CRISPRi-based Screen of Unfolded Protein Response (UPR) Using 3' sgRNA-CR1cs1Cell surface protein labelingCITE-seq; 8k Cord Blood Mononuclear Cells with 13 AntibodiesASAP-seq; Multiplexed CRISPR Perturbations in Primary T Cells1k Human PBMCs Stained with a Panel of TotalSeq B Antibodies, Dual IndexedECCITE-seq6k Single-cell Multimodal Readout of NIH-3T3, MyLa, Sez4 and PBMCsPHAGE-ATACAnti-CD8 Phage Hashing Single-cell ATAC-seq Using CD8 T Cells from Four Human DonorsCellPlex10k 1:1 Mixture of Raji and Jurkat Cells Multiplexed, 2 CMOs30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei Multiplexed, 12 CMOsCell hashingPeripheral Blood Mononuclear Cells with 8 AntibodiesMULTI-seq15k HEK293 and 40k HMECs Multiplexed by Lipid- and Cholesterol-tagged IndicesTargeted transcript enrichmentHodgkin's Lymphoma, Dissociated Tumor: Targeted, Gene Signature PanelPseudo-bulk10k A375 Cells Transduced with (1) Non-Target and (1) Target sgRNA, Dual Indexed10k 1:1 Mixture of Raji and Jurkat Cells Multiplexed, 2 CMOsUsage$ fba

usage: fba [-h]  ...

Tools for single-cell feature barcoding analysis

optional arguments:
  -h, --help        show this help message and exit

functions:

    extract         extract cell and feature barcodes
    map             map enriched transcripts
    filter          filter extracted barcodes
    count           count feature barcodes per cell
    demultiplex     demultiplex cells based on feature abundance
    qc              quality control of feature barcoding assay
    kallisto_wrapper
                    deploy kallisto/bustools for feature barcoding
                    quantificationextract: extract cell and feature barcodes from paired fastq files. For single cell assays, read 1 usually contains cell partitioning and UMI information, and read 2 contains feature information.map: quantify enriched transcripts (through hybridization or PCR amplification) from parent single cell libraries. Read 1 contains cell partitioning and UMI information, and read 2 contains transcribed regions of enriched/targeted transcripts of interest. BWA (Li, H. 2013) or Bowtie2 (Langmead, B., et al. 2012) is used for read 2 alignment. The quantification (UMI deduplication) of enriched/targeted transcripts is powered by UMI-tools (Smith, T., et al. 2017).filter: filter extracted cell and feature barcodes (output ofextractorqc). Additional fragment filter/selection can be applied through-cb_seqand/or-fb_seq.count: count UMIs per feature per cell (UMI deduplication), powered by UMI-tools (Smith, T., et al. 2017). Take the output ofextractorfilteras input.demultiplex: demultiplex cells based on the abundance of features (matrix generated bycountas input).qc: generate diagnostic information. If-1is omitted, bulk mode is enabled and only read 2 will be analyzed.kallisto_wrapper: deploy kallisto/bustools for feature barcoding quantification (just a wrapper) (Bray, N.L., et al. 2016).