gartner-lab / demultiplex2 Goto Github PK

Hey Qin and Danny,

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

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!