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
I used Download and Extract Reads in FASTQ format from NCBI SRA for my SRR data. I know that my data is a paired end as collection. However in the trimmomatic function when i choose paired end as collection the drop down list says
Please provide a value for this option.
Select FASTQ dataset collection with R1/R2 pair *
However, this is highlighted in blue and I am not able to select anything for this option even when my data is in Fastqsanger.gz format.
So im confused as to what to do next and how to get trimmomatic to run.
here i included pictures of what im trying to do and my data set
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.