Problem: "Pair-end" reads scRNA seq data (Drop-seq)
I received the following message from the author of another Drop-seq paper:


  After much conversation with the folks at the SRA, it appears the SRA
  compression algorithm automatically deletes certain subsets of bam
  tags and does so in cryptic way (in the sense of not alerting the
  uploader). Obviously this is going to be an issue for many single cell
  datasets encoded this way, and I hope the SRA will eventually change
  their system to accommodate.


If you look at the "Download" tab of the same page, there now exists a link to download the originally uploaded BAM file.

Alternately, you can use the SRA AWS tutorial to download the files on that platform.