3 votes

How to handle technical replicates in cellranger count?

It depends what you mean by "technical replicates". If it is the exact same library prep spread out over two lanes, or two flowcells, they must be combined at the fastq stage. Cellranger ...
swbarnes2's user avatar
  • 1,925
2 votes

How to handle technical replicates in cellranger count?

If they are truly technical replicates in the most specific sense (e.g. from the same extraction and library prep, just split up for sequencing), then the counts for each identified cell can be ...
gringer's user avatar
  • 14.1k
2 votes

problem with running Kallisto on single cell data

created another environment called "kb", where I installed Kallisto-bustools This is known to work well. What about installing bustools in the same env as Kallisto? Alternatively you can ...
M__'s user avatar
  • 12.3k
1 vote

How to import data from cell ranger to R (Seurat) using Read10X?

It is been a while since the last time I have done this, but the problem seems to be your filenames. For example Read10X() is expecting a file ...
haci's user avatar
  • 4,112
1 vote

problem with running Kallisto on single cell data

Well, it's embarassing to say but...I didn't have Autotools, CMake, and Make installed! Once I installed them, I could run the command. However, I am running now in another problem: even though the ...
Simon's user avatar
  • 31
1 vote

Low fraction reads in cell metric in snRNA-seq data

Yes, "low fraction reads in cells" is more common with snRNA-seq from frozen samples, I wouldn't worry about it by itself (you're just throwing away some sequencing data). You should still ...
Chris_Rands's user avatar
  • 3,948
1 vote

Low custom tdtomato gene content

I am unable to respond to other's comments as I never usually comment, so this is a new account. However, I spent the last couple days really diving into the BAM alignments when mapping scRNAseq reads ...
El_Rey's user avatar
  • 11

Only top scored, non community-wiki answers of a minimum length are eligible