I want to retrieve a subset of FASTQ reads from SRA data sets in my History. Previously, I used fasterq-dump to import 4 SRA data sets into my history (e.g., SRR10201511) as a collection named “Pair-end data (fasterq-dump)”. I have a separate file with a list of ~120k read accession IDs (e.g., SRR10201511.1.1), and I now want to extract the fastq records with these accession IDs from the SRA data sets.
I tried to use the Filter list tool in the Collection Operations section with the Input Collection set to “Pair-end data (fasterq-dump)” and Filter out identifiers absent from set to the uploaded text document with the list of read accession IDs (each ID on a separate line), but apparently this tool is used to retrieve complete data sets (e.g., SRR10201511) from a collection.
I see that the Filter FASTA tool has the option “Criteria for filtering on the headers” where you can supply a list of IDs, but the Filter FASTQ tool does not; you can only filter reads based on quality score and length.
Is there another tool available that can be used to retrieve the desired subset of reads from a fasterq-dump data set?