Good morning everyone, I am new to bioinformatics and all related fields. I was given a scRNA-seq data with format: read 1 contains 16 barcodes, 10 umi and 124 bp, read 2 contains 150 bp. I think the data are generated from the following protocol: Base Composition of Sequencing Reads of Chromium Single Cell V(D)J Libraries I was asked to perform alignment and quantification. Can someone please tell me how to do that? Thank you so much for your kind help!
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tomleee012 •
10X genomics has a great pipeline called Cell Ranger that will perform all of the QC, alignment, and counting. Importantly, at the end you will have a folder called filtered_feature_bc_matrix for every sample that has the cell barcodes, features (genes), and count matrix that can be used for downstream analysis in Seurat, Bioconductor, Scanpy, etc.
Thank you very much! It works very well! I have algorithms other than the default Seurat to model the data matrix.
I don't mean to criticize anyone in particular, but let's just say that your situation is less than optimal. Without knowing the whole story, it appears that you are given the data of uncertain type and/or origin, and you are asked to do something you don't know how. But that's not even half the problem, as this is not just a matter of doing things that are not familiar. If you asked how to make a Mediterranean rack of lamb, there would be a recipe and/or video that would help you complete the task by simply mimicking what others are doing. The thing is that there are no positive and negative controls in cooking, nor is subsequent result interpretation required.
I will suggest to you the same thing I have already told many people in your situation: find local help, someone who can explain things as you move forward. And before anything else, make sure that you know what's in your data.
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