There are many previous threads regarding how to retrieve selected raw reads from fastq files offline; does anyone know of a public galaxy instance with a tool that can return a set of raw reads using a query of post-filtered, post-mapped reads?
Convert fasta/fastq to tabular format (Convert Formats) then perform a Join between the list of sequence IDs on your file and the first column of the new tabular dataset (representing sequences). At the end convert the extracted sequences from tabular back to fasta/fastq.
Extract this protocol, once in your history, into a workflow for re-use if it is an operation that will be reused.
Thanks, Jen, Galaxy team