Fastqsanger.gz is not working in the trim galore or trimmomatic flexible trimming tool as a paired end collected. Ive tried to use a D interlacer to get it to work but the drop down list doesnt allow me to select my SRA data. Is there something i could do to fix this?
Items to check:
First, be sure that you are using the option on the tool forms to look for collections of input reads. faqs/galaxy/#selecting-a-dataset-collection-as-input
If the form is looking for a collection but doesn’t find your specific collection, next check that the individual files in your collection were assigned a datatype that matches the input field on the tool form.
Why the Fastq De-interlacer tool would help is not clear. Is the existing collection a list of datasets? Or a list of dataset pairs? If the reads are already split into pairs, then you won’t need that tool.
This tool is a great way to get reads from SRA into Galaxy that are sorted into collections: Faster Download and Extract Reads in FASTQ format from NCBI SRA
These tutorials can help more.
If you are still stuck after reviewing, and please create a shared history link and post that back in your reply. faqs/galaxy/#sharing-your-history. Leaving all datasets undeleted, including your tests, will help to get the best feedback from our community.
Let’s start there
That dataset is a single file, not a collection. It is an interleaved paired-end dataset.
The NGS data logistics tutorial linked above covers this type of file. It can be produced by the Download and Extract Reads in FASTA/Q format from NCBI SRA tool.
Try using this tool instead to extract the reads into collections → Faster Download and Extract Reads in FASTQ format from NCBI SRA.
The tool names are similar, and retrieve similar data, but the “Faster” version will sort the output into collections.