Simoni Tiano

Do I use scrublet after doing the standard preprocessing from Seurat?

1

I am trying to figure out at which point I should use scrublet. Am I supposed to do it after doing the standard preprocessing from Seurat and then import the...

Question about kallisto indexes

3

Hello, I was wondering if it is more appropriate to use the v1 standard kallisto index https://github.com/pachterlab/kallisto-transcriptome-indices/releases for bulk RNA seq data compared to an index created by concatenating Mus_musculus.GRCm39.cdna.all.fa.gz...

Question about assigning gene names using t2g file

1

Hello, I am working with bulk RNA seq data. I created a reference like shown below: `kallisto index -i mouse_version111cdna Mus_musculus.GRCm39.cdna.all.fa.gz` Then I created a t2g file using a script...

I run scrublet on my data and I noticed afterwards that the barcode names had changed. For example, AGAAGCGGTGGTCTGC-1 became AGAAGCGGTGGTCTGC-1-0 and AGAAGCGGTGGTCTGC-1-1 became AGAAGCGGTGGTCTGC-1-1-1. Is that normal? Thank you