SRA dataset to Seurat Object
I have this dataset downloaded in fasta files using SRA toolkit in windows.
How can I
- merge all lane1 (fasta1) files into 1 file?
- merge all lane 2 (fasta2) files into 1 file?
- use the above merge files in RNAStarsolo?
Basically, I want to convert the above dataset into a Seurat object.
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you mean in
FASTQformat, right? And for each sample you have twoFASTQfiles, why would you merge them?i have 35 samples . so each sample has two .fasta files so how can I read them into seurat as one object ?
You mean
FASTQfiles. You have to process them before getting into Seurat. You have to align those reads first, then annotate them, and finally generate the sparse matrix for each sample. Once you get the matrices, you can then load them into Seurat. Check their paper to see how they processed the raw data, they should indicate what is the tool used to generate the matrices.