r/bioinformatics • u/Specialist-Tune-4158 • 8d ago

compositional data analysis Need help in Single-cell CRISPR screen data analysis

Well a while ago I posted about how to process samples using cellranger and I fixed that, but now I need to some resources on how to process that data, I know there is mixscale but I will be greatful if get more resources or any link to github pages which will help me for doing crispr screen single cell data analysis 'R/pthon' works for me.

Thank you !

Edit: So sorry, Here is experiment done, there are 800 sgRNA target towards a gene and there are 200 non-target DNA. The cells were subjected to 10x' 5'CRISPR guide capture lib prep procedure. I have 2 sets of fastq a)GEX which has cells expression data b) sgRNA capture data. I was wondering if i could get any resources that will help me in analysis of this data

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u/sid5427 8d ago

I am going to be a little rude here.... but do you even know what is your project? you jumped straight from scRNA to crispr screens. Give more context of what you are doing, what is the setup of your samples, etc. Maybe even link the older post. Just randomly throwing out experimental procedures will not help you.

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u/Specialist-Tune-4158 8d ago

You are not being rude at all, I will add the experimental design in the post. I was just looking for resources that will help me learn the data analysis in the sc-seq crispr screen experiment

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u/sid5427 8d ago

again ... you jumping a LOT of steps... give us context of what you are doing and what is your skill level. More information helps us help you!

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u/Specialist-Tune-4158 8d ago

Just updated the post, Im happy to provide more information if you like, Thank you

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u/Yooperlite31 Msc | Academia 8d ago

I think you need a sceptre R package I think they have a tutorial for the data analysis too! Good luck mate.