I have a question related to processing of Single cell RNA-seq data originating from non 10x platform. I have worked with data that originated from 10x platform and I parse it through cell ranger pipeline and then put it through Seurat.
As an example the dataset in this GSE156644 repository are not being processed through Cell ranger pipeline and I get an error that indicates "single-end read found" another example is of this GSE115235, in the later I have bunch of files that look like bulk RNA-seq.
If you check the GSE115235 it has bunch of files that are not cellranger compatible. However, they are from single cell experiment. I find it strange that NCBI accepts such submission and the reviewers don't even pay attention to what has been submitted.
I guess, that these are SE RNA seq data that can be aligned using STAR or Bowtie and then merged in some way to get per cell per sample expression.
Along similar lines, how do I deal with 2 fastq files for a scRNA seq run? example https://www.ebi.ac.uk/ena/browser/view/PRJNA602526
This link has scRNA seq files that look paired end (R1 & R2 but NO I1). I am bit confused as cell ranger count option requires the folder to have 3 files (I1,R1,R2). How can I run cell ranger with R1 & R2? Or do I need to use another aligner?
I will send an email to sra and also to the authors, but any other help to navigate through these datasets and process them is deeply appreciated.