Fastqcdump file issue

[Muhammad_Azhar]

Dear all, I have downloaded GSE dataset in SRA format directly into History of my login in galaxy server, the data showed single end and paired files, but single end files are empty, but paired end files exists in paired end files can be seen by clicking on them, So FASTqc and Mulitgc ,Fastp not picking paired end files cz may be all the tools needs direct paired end files in hsitory so how to directly extrqact or use paired end files ?

[jennaj]

Welcome, @Muhammad_Azhar

QA tools will expect reads in fastqsanger or fastqsanger.gz format. You can use SRA accessions to extract from NCBI and that sort of data will be download.

These tutorials have examples:

GTN Materials Search

Getting Data into Galaxy

Data Upload Use the Upload tool to load datasets into your history Files from your computer using Choose local files Files with a public URL using Paste/Fetch data Files from remote data sources using Choose remote files files can be dragged and dropped to launch the Upload tool! More choices include Use a data retrieval tool to load files into your history. See the tool panel for these options Copy datasets from Shared Data → Data Libraries into your history Batch Upload All servers support a resume function directly through the Upload tool for very large local data loading. Data retrieved through all other methods is entirely remote and performance is dependent on the connection between that other service and the Galaxy server where you are working. UseGalaxy.org offers the custom command-line galaxy-upload function. FTP Upload is available at some services, including UseGalaxy.eu and UseGalaxy.org.au. Q&A I tried to retrieve a batch of accessions from NCBI SRA, but the query failed! First, check your query terms. Most of these underlying tools expect one accession term per line without any extra spaces or blank lines. You can confirm by reviewing the tool form instructions. Next, try again! External data services can get busy and reject queries for unclear reasons. Trying again at a different time is a common solution. References Using Galaxy and Managing your Data Upload FAQs at https://training.galaxyproject.org/training-material/faqs/galaxy/#data%20upload https://github.com/galaxyproject/galaxy-upload The usegalaxy.org FTP service will be decommissioned on August 12, 2022 https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting_reporting.html Any persistent problems can be reported in a new question for community help. Be sure to provide enough context so others can review the situation exactly and quickly offer advice. Consider https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html or posting content from the Job Information view as described in https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html.

If that is not enough to resolve the problem, maybe some screenshots from you would help to clarify what is going on? But please do review the tutorials first since I’m guessing something went wrong with how the reads were loaded if empty!