SRR number not coming in as one single fastq dump file but single end file

usegalaxy.org support
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Hi @HG123

This accession has two technical reads and one biological read per spot.

  1. The NCBI tools are sorting the read data in different ways.

  • Faster Download and Extract Reads in FASTQ is only extracting the single biological read with the default settings. That single biological read is sorted into a single-end collection.

  • Download and Extract Reads in FASTA/Q is extracting all three reads into one result dataset. It sounds like this is what you want from your examples.

  1. Alternative is to capture the URLs from the data source and paste those into the Upload tool: Run Browser : Browse : Sequence Read Archive : NCBI/NLM/NIH. This would be the same results as the Download and Extract Reads in FASTA/Q tool.

Once you have the reads uploaded, sort them directly and optionally create collections. Examples of how to sort read by identifiers are in this FAQ. Use the regular expression matching options, not the “de-interlacer” tool.

Related Q&A: Failing to load single-cell raw fastq files into Galaxy

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