Obtain read counts from Qiagen GeneGlobe

Question

[Abhishek]

Hi all,

I used Qigen Gene Globe RNA seq portal to obtain read counts from the fastq files I had.

The "Align and Count" step has been completed and it correctly lists the number of samples and sample names. But I'm unable to find an option to download the excel sheet containing read counts / UMI counts of the transcripts for all the samples.

I had previously obtained such a file from the one who had done the experiments. (It was an excel file with multiple sheets and one sheet of interest - 'miR_piRNA' containing read counts and UMI counts for all the transcripts in all the samples). Its my first time trying to use GeneGlobe myself. Has the user interface for GeneGlobe RNA seq portal changed recently ? This link still mentions the excel sheet : https://www.qiagen.com/au/resources/download.aspx?id=bea2dcfa-0a5c-47c5-afd8-8b0fe90a471a&lang=en

Can someone please share a screenshot / steps on how to download read count data from Geneglobe ?

Answer 1

[Abhishek]

Answering my own post for benefit of others. The default option in Qiagen GeneGlobe --> Analyse Data --> Start Your Analysis gives the result I mentioned above.

To get the excel sheet I wanted with all transcripts for all samples, before clicking "Start Your Analysis", change the option under "Select analysis pipeline" from the default "RNA-seq Analysis Portal" to "Legacy Analysis Pipelines"

[George]

My apologies for the delayed follow up, but I was only made aware of your post today. You are correct that the RNA-seq Analysis Portal currently does not report on the expression level of the individual piRNAs, but only the total number of piRNA reads in each sample, unlike our "legacy" QIAseq miRNA Quantification Analysis application. Since your post, we are discontinuing the legacy application, but we are also working to add features missing from the newer RNA-seq Analysis Portal relative to the legacy pipeline, including reporting the expression of individual piRNAs. While I do not have a timeline for that new version release, we are still providing access to the legacy application for customers who still need it. As the Product Manager for all the GeneGlobe Analysis applications, including the RNA-seq Analysis Portal, I can help you with access and any other questions or needs that you have. Please feel free to reach me at [e-mail]. For future reference, there is a "Contact support" link under the Help menu in the top right corner of the RNA-seq Analysis Portal that will get in touch with our bioinformatics technical support team for faster service. Thank for raising this question here.