zgb963

Problems with running Liftoff on HPC environment

4

Hello, I've been having issues running Liftoff. It's taking days to run and then terminates. I'm running it on an HPC environment using 100GB memory and a computer node that...

GFF does not contain any gene features. Use -f to provide a list of other feature types to lift over.

4

Hello, I'm using hg38 GTF from NCBI and ran liftoff with the Rhesus macaque FASTA and hg38 FASTA. ``` liftoff liftoff/rheMac10.fa liftoff/hg38.fa -g liftoff/hg38.ncbiRefSeq.gtf -p 10 -o liftoff/update_rhemac10_lifted.gtf ``` Here...

Change orig.ident column in seurat meta.data to match cell barcode sample prefixes

2

Hi Seurat Team, Do you know how I can change the orig.ident column of the seurat meta.data so that it can differentiate between the 4_D_MI2_S2 and the 4_MI1_S5 sample? Right...

Can't run identify_empty_drops function

1

Hello I was previously trying to use the identify_empty_drops function on my sample output from 10X cellranger count pipeline but it doesn't seem to be working. I've put an example...

Python errors when running lifton

2

Hello, I'm having an issue with running the lifton software. I'm running it on an HPC environment using 100GB memory and a computer node that has 2000 cores. The below...