Tag: mkref
Create customized gene annotation file
Create customized gene annotation file 0 Hi, I have self-defined RNA sequence, it was used to tag the special cells I’m interested in. I want to use cellranger mkref to build a custom reference and use this reference file to count the cells that have this sequence. Do you have…
Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants
Data reporting No statistical methods were used to predetermine sample size. The experiments were not randomized. The investigators were not blinded to allocation during experiments and outcome assessment. Study approval This study and all the relevant experiments were approved by Guangzhou Eighth People’s Hospital Ethics Committee (No. 202001134 and 202115202)….
transcriptome – How to combine multiple .fasta files of primary assembly from Ensembl into one for sequence alignment?
I have some marmoset snRNA reads that I want to align with the reference transcriptome using cellranger. The primary assembly for marmoset is available here, which is broken down into 22 parts. However, cellranger mkref only accepts one .fa file to generate the transcriptome. I tried concatentaing all the extracted…
Your reference doesn’t appear to be indexed. Please run the mkref tool.
cellranger-dna: Your reference doesn’t appear to be indexed. Please run the mkref tool. 1 I received the following error when running cellranger-dna: “Your reference doesn’t appear to be indexed. Please run the mkref tool”. The reference that I used was downloaded from 10X database. I thought the reference was already…
