Code for analyses in the STARsolo manuscript
Directories contain:
data: 10X cell barcode passlists
samples: scRNA-seq data make -C samples # downloads real data
exe: tool executables make -C exe # downloads executables
genomes: genome files and indexes make -C genomes # downloads genome FASTA/GTF and builds indexes for all tools
sims: simulated data pipeline make -C sims # generates simulated data, saves FASTQs in the samples/
count: contains the results of runs make all # will run all tools on all datasets. Benchmarking will take a really long time make real # will run all tools on the real dataset(s) make sims # will run all tolls on the simulated datasets
compare_matlab: comparison figures for simulated and real data compare_real_pbmc5k.m # real data comparison compare_sims_pbmc5k_mgNo.m # simulations without multi-gene reads compare_sims_pbmc5k_mgNo_OnlyExR.m # simulations without multi-gene reads and without exonic reads compare_sims_pbmc5k_mgYes.m # simulations with multi-gene reads
preprocess_scanpy: preprocessing of the count matrices: load, select common cells, normalize python real_pbmc5k.py
clusters_scanpy: clustering and DGE python clusterDE_pbmc5k.py
clusters_matlab: DGE figures DE_pbmc5k.m: plots DGE figures