I downloaded some single cell RNA-Seq data from SRA sites. Unfortunately, only the R2.reads (~100bps) was uploaded for all the SRR files (SRR11573310...).
I am wondering if anyone would know if it will be ok to align the reads to genome just like regular RNA-Seq pepline. For example, use hisat2_htseq-count to achieve the gene counts?
Thank you very much for any the help!