Access sequence data of clustered scRNA analysis

Question

[bianca.pircher]

Dear all,

currently I am analyzing a certain cell type of the mammalian retina. In addition to my 'regular' methods I want to underline the results with a sequence analysis. I have found a good study providing the results of a scRNA sequencing: https://singlecell.broadinstitute.org/single_cell/study/SCP301/c57b6-wild-type-p14-retina-by-drop-seq#study-summary https://www.ncbi.nlm.nih.gov/sra?term=SRP050054

Is there a way to directly access the clustered data, i.e. to access the sequence information of a single cell?

Thank you so much!

Best, Bianca

Answer 1

[swbarnes2]

The bam files in theory could have reads annotated with both their cell barcode and gene ID, but it looks like the SRA only has fastqs, which means you'd have to do the whole analysis over again. Maybe you could ask the authors for the bams?

The read data in single cell experiments is very spotty, especially at the level of individual genes. The reads might even be biased towards one end of the transcript or the other, so the sequence you want to examine might not even be represented at all. I don't think you will learn much at all.