search

Gartner-Lab / deMULTIplex2

deMULTIplex2: robust sample demultiplexing for scRNA-seq
Creative Commons Attribution 4.0 International
10 stars 0 forks source link

Demo dataset #82

Closed fangx26 closed 1 year ago

fangx26 commented 1 year ago

Hey Qin and Danny,

Could you guys also upload the test multiplexing library FASTQs to Github? Thanks you very much.

qinzhu commented 1 year ago

Hi, We have prepared a demo dataset. See below for a complete code example with fastq files from McGinnis et al(Download from https://github.com/Gartner-Lab/deMULTIplex2_test_data/): 

fastq_dir <- "McGinnis_BAR_fastq/"
read_table <- readTags(dir = fastq_dir,
                       name = "TGACCA",
                       barcode.type = "MULTIseq",
                       assay = "RNA")

data(multiseq_oligos) # Current MULTI-seq oligo sequence provided with the package
tag.ref <- multiseq_oligos
tag_mtx <- alignTags(read_table, tag.ref)
cell_ids <- Matrix::rowSums(tag_mtx) > 100 # Filter for cells (it's better to use your own cell filter criteria based on RNA count)
tag_used <- Matrix::colSums(tag_mtx) > 1e4 # Filter for used tags
tag_mtx <- tag_mtx[cell_ids,tag_used]

res <- demultiplexTags(tag_mtx,
                       plot.path = "./",
                       plot.name = "demux2_",
                       plot.diagnostics = T)

Let us know if you have additional questions.