Perturb seq
Hi I am new to single cell CRISPR analysis. I ran the sequencing files on 10x cloud and have two donors (15 & 16) with three timepoints - baseline, early and late. I have filtered h5ad files for each sample and protospacer calls per cell file for each sample. how do I assign gRNA to cell , is there a tool to this? can I run scmageck or scepter on this dataset , I don't know how to assign gRNA prior to running scmageck. is there a threshold method how does it work and does anyone have code or links to tools that do this?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
feature_ref files in upstream analyses related to Perturb-seq
written by 2443422660 •
-
How to concat multiple h5ad files into one
written by Bioinformatics_begginner •
-
Cell ranger multi for demultiplexing FB files and GEX files
written by shlo12 •
-
Can I infer the fraction of replicating cells from bulk RNA-seq data?
written by txema.heredia •
-
best practices for integrating
written by Nal23 •
-
Aggregating multiple 10 X samples count matrices into one before analysis.
written by chanukyapavan4287 •
-
How to demultiplex single cell rna-seq based on SNP mutation?
written by ahmad mousavi
-
Automating Workflow with multiple Inputs and Differing Variables
written by tropeedward •
-
How to analyse data from genetic screening followed by NGS ?
written by Assa Yeroslaviz
-
Suggestions for RNA seq pipeline
written by sangita_b
While you wait for answers a search brought up this analysis workflow: https://satijalab.github.io/Mixscale/