Query qbout single cell sequencing

Question

[abbas.waseem.gcu]

I am a new student working with scRNA seq data regarding which I have a few queries. Can single cell rna-sequencing both single end or paired end?

If paired end then what information is in _1 and _2 fastq files because I have gone through a list of datasets in which _1 contains barcodes and UMI information and _2 contains reads.

I am dealing with a dataset in which both _1 and _2 files contain reads of 151 bp length , is it paired end? If yes then how to identify the barcodes for fastq files and are there separate barcodes for both _1 and _2 files.

[GenoMax]

Please do not post identical content in multiple threads. Ref old thread: ScRNA data

That said. If you are planning to use cellranger it should take relevant part of the read (28 bp) that it needs from read 1, if this is 10x genomics data. Just saying scRNAseq is not enough. Which technology is the data from?

[abbas.waseem.gcu]

The data is from 10X Genomics platform with combined barcodes, UMIs and cDNA in both files. I am trying to use rna STARsolo on galaxy but when i select the option files with barcodes and cDNA combines the tools says no fastq files available. Please guide me how to use rna STARsolo and my dataset is GSE149512

[Ram]

Show us your exact cellranger and STARsolo commands, the full output to STARsolo as well as your thoughts on why it's not working for you.