SRA Downloads a Single FASTQ File for Paired-End Reads Which Is Not Compatible with Kallisto Workflow

[erguntiryaki]

Hello,

This issue is not related to Kallisto/BUS but I am writing here because I couldn't reproduce the RNA velocity tutorial. When fastq files are properly provided, Kallisto and other tools just work well. However, sra-tools download paired-end libraries as a single fastq file despite the --split-files option when the fastq-dump command is called. I am wondering how can we download properly formatted paired-end reads to work with Kallisto.

The authors provided nice formatted fastq files in the RNA velocity tutorial. How can I download the same formatted files from SRA?

Thanks in advance.