I am new to Galaxy and bioinformatics so feel free to let me know if there is a better way of asking my question. The files were executed in a way that the MultiQC did not recognize the files existed. I downloaded SRA files to Galaxy. These files were transfered to a Paired-end data folder with each accession (sample) inside along with the forward and reverse fastq files. This general file format remains after running these Files through FastQC. Now, I am trying to run the files through MultiQC but the data is not recognized. Does anyone have suggestions on how to fix this?
Please see this tutorial https://galaxyproject.org/tutorials/ngs/#organizing-and-qcing-multiple-datasets for:
- How to create fastq dataset collections
- How to run FastQC in batch on collections
- How to generate a MultiQC report based on those FastQC results in a collection
Double checks: Make sure the MultiQC tool form is set up correctly for this use case (all covered by the video in the tutorial):
- FastQC reports are in a dataset collection
- “FastQC” is set as the report type.
- “Dataset Collections” are set as the input type.
- Pick the “raw” results (text report). The “html” results are not appropriate.
My guess is that either item 2 or 3 was not set properly on the FastQC tool form.
admin edit: Cross-posted at Gitter: https://gitter.im/galaxyproject/Lobby?at=5c0c5f88178d7860a1a84938