Failing to load single-cell raw fastq files into Galaxy

I am trying to use Faster Download and Extract Reads in FASTQ to download single-cell RNA-seq raw reads. The specific SRR accession is SRR11821880, and the SRA run browser tells me that there are three reads per spot. The first two are technical reads (adapter: 8 bp, barcode+UMI: 28 bp), and the last one is a biological read (150 bp).

My settings for the tool are:

  • Select input type: SRR accession
  • Advanced options>Select how to split the spots: --split-files
  • Advanced options>Dump only biological reads: No

Currently, I am only getting the fastqs with the adapter sequences and the biological reads, but not the barcode+UMI. Iā€™m unsure of why this is happening, since I am able to browse and view all of the reads in the run browser. Is this tool restricted to getting only two files maximum, or am I overlooking a setting?

Hi @cathy37,
it seems that is not possible to get the 3 reads at all, and the ENA dump also just contains 2 fastq files.

If you go to, under data access you can get the original files, that might be the easiest way to get them.


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