Conversion of a tar file to fastq format

Hello!

I am trying to convert a tar file from GEO to a fastq file to perform Pathway Enrichment Analysis using Galaxy. However, I am not able to do so in Galaxy. Can anyone help in solving this issue?

Welcome, @rib_b

When Uploading a tar file to Galaxy, only the first file will be loaded. That can sometimes just be an indexing file, not the actual read data.

Try uncompressing the data locally, then Uploading the individual files to Galaxy. Use all defaults for fastq reads. How to guide → Getting Data into Galaxy

If you want help confirming what to do, you can share back a URL to the data and we can try to help more. Thanks! :slight_smile:

Hello! Thank you so much for your response :slight_smile:

I am trying to convert the following dataset to a fastq file.

I am trying to use the RAW http formatted tar file. Can you help with this?

Hi @rib_b

Great, thanks for sharing the link.

So, for this GEO series … the raw files are not available, only the processed expression values.

In general, this is how to get batches of sequence read data into Galaxy from the public archives. The process won’t work for this data since there isn’t any read data to retrieve but maybe it will help later on. :slight_smile: Using Galaxy and Managing your Data / Tutorial List