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bm2-lab / MUSIC

model-based understanding of single-cell CRISPR screening
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About the format of list of gRNA #2

Open Lindky opened 5 years ago

Lindky commented 5 years ago

I didn't find any information about how did you generate these two files: cbc_gbc_dict_grna.tsv, cbc_gbc_dict.tsv, it can't be generated from 10X genomic cell_ranger. I know these two files are the information of sgRNA although it shows no much different. I create my own sgRNA information file based on the format of yours, however, it shows an error when I run the MUSIC in R: Error in strsplit(perturb_information[i], ",") : non-character argument

Could you give me more information about how did you create these files?

Lindky commented 5 years ago

I fixed the problems. Just make a little change on your original code: sample_info_arr <- unlist(strsplit(as.character(perturb_information[i]),",")). BTW, other code might also be fixed since it shows errors when the people use the newest version of 10X genomics and Seurat.

yysheep2020 commented 4 years ago

Hi, I would like to ask when you use "cellranger count" function, did you make the ref genome by yourself. More specifically, do we need to add sgRNA sequence into the human reference genome?

gwaybio commented 3 years ago

I didn't find any information about how did you generate these two files: cbc_gbc_dict_grna.tsv, cbc_gbc_dict.tsv

I am also running into this error when using MUSIC::Input_preprocess_10X() as described in #3