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License: Creative Commons Attribution 4.0 International
deMULTIplex2: robust sample demultiplexing for scRNA-seq
License: Creative Commons Attribution 4.0 International
Hi,
I tried to use deMultiplex 2 package for my MULTI-seq data.
However it returns Fitting Failed for my first tag group but works fine for other tags.
Do you guys have any idea why does it happen?
PS: I tried to use another dataset and it works fine too.
rm(list=ls())
data1 <- Read10X('/Users/admin/R/day3raw_feature_bc_matrix')
10X data contains more than one type and is being returned as a list containing matrices of each type.
tag_mtx <- t(data1$Multiplexing Capture
)
data(multiseq_oligos)
tag.ref <- multiseq_oligos[3:6]
cell_ids <- Matrix::rowSums(tag_mtx) > 100
tag_used <- Matrix::colSums(tag_mtx) >1e4
tag_mtx <-tag_mtx[cell_ids, tag_used]
res <- demultiplexTags(tag_mtx, plot.path ="./", plot.name = "demux", plot.diagnostics = T)
Running EM for TDBonly
Iteration 1; Q diff: 41543.1943022717
Fitting failed.
Running EM for TDBUrelumab
Iteration 1; Q diff: 41702.5440420353
Iteration 2; Q diff: 3491.6057314845
Iteration 3; Q diff: 4585.20532365606
Iteration 4; Q diff: 493.522236918252
Iteration 5; Q diff: 128.96474546846
Iteration 6; Q diff: 336.784192556333
Iteration 7; Q diff: 91.3320290341871
Iteration 8; Q diff: 32.8050920890091
Iteration 9; Q diff: 0.000563061577850021
Getting the following error installing:
Error: package or namespace load failed for ‘deMULTIplex2’ in namespaceExport(ns, exports):
undefined exports: downsample_mtx
Looks like you removed the function but it's still in your namespace file. Just FYI! I'll install by downloading/cloning for now.
Hi,
For sci-Plex
, the cell barcode position is not a fixed value.
R1: { 9-10 bp hairpin barcode }-{CAGAGC}-{ 8bp UMI }--{10 bp RT barcode}
How could I generate the readTable
for this read structure?
Thanks for your excellent R package! It is such a great help for bioinformatic beginner like me!!
Any reply would be really appreciated!
Hey Qin and Danny,
Could you guys also upload the test multiplexing library FASTQs to Github?
Thanks you very much.
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