search

timothy-barry / sceptre-pipeline-1

The sceptre Nextflow pipeline.
1 stars 3 forks source link

Dataset_input #5

Open VeronicaYumiceba opened 1 year ago

VeronicaYumiceba commented 1 year ago

Hi Timothy, I am completely new in bioinformatics and now I have data on 10X CRISPR screen to analyse. I will like to use sceptre Nextflow tool. Before using my data I will like to go through the "Gasperini data 2019". I am not sure where to get the data from or how did you format the data submitted on GEO: GSE120861 from the paper. Thanks

timothy-barry commented 1 year ago

Hi,

Would you mind providing a bit more information about your data? What is the MOI? How many cells are there? How many targeting and non-targeting gRNAs do you have?

Have you worked through the low MOI sceptre tutorial yet? My recommendation would be to work through the low MOI sceptre tutorial to get familiar with the package. Then, assuming you have high MOI data, I would recommend analyzing your data using the run_sceptre_highmoi_experimental function within R. The interface to this function is very similar to that of the low MOI function.

I would view the sceptre Nextflow pipeline as a last resort. We can try to deploy this pipeline on your data if the run_sceptre_highmoi_experimental fnction does not suit your needs, but the Nextflow pipeline is in a very early stage of development.

VeronicaYumiceba commented 1 year ago

Hi Timothy, Thanks for you reply. The data I generated came from a CRISPRa assay 10X feature barcoding CRISPR screen. I have run the first pilot experiment with 118 gRNA (~3gRNA per loci), 20 non-targeting/random gRNAs and 44 positive controls TSS gRNAs. According to Cell Ranger I analysed ~22.000 cells. Most of the cells got 1-3 gRNAs but I have also cells with several too, so I will like to use the high MOI approach as in the future assays we aim high-MOI/throughput. I went through the tutorials for low and high MOI and based on your recent paper in Science I thought the input data were 2 Seurat objects: Gene Expression and CRISPR library. One of the questions that came to my mind while running these tutorials is why are the gRNAs grouped by target instead of analysing them separately? In case of further questions my email address is: veronica.yumicebacorral@student.uni-luebeck.de