Galaxy tool for quantifying RNAseq data

[mlk]

Dear all,
I'm new at RNAseq data analysis and would appreciate your help.

*I'm looking for a tool for quantifying my RNAseq data (Illumina pair ends), that should be: 1. available at the Galaxy interface (Melbourne server) 2. will normalize the data to both library size and to CDs length (cause I want to be able to compare genes within the sample but also across treatments) 3. input/work with genome alignments (preferably HISAT2), and not with alignments to transcriptome (the transcriptome that is available for my organism is problematic).

* I manually calculated TPM values in Excel (using the count matrix and lengths achieved with featureCounts tool). the issue is how can I do statistics for the TPM values? (replicates and adj pval)

does anyone has anything in mind for other one of the approaches?

Thank you in advance!

[ashishbansal]

Trackster is a visual analysis environment that is integrated into Galaxy. We have used Trackster’s interactive visualization capabilities to analyze high-throughput transcriptome sequencing data. Using Trackster, Cufflinks was repeatedly run to identify the parameters that yielded that best transcript assembly, and dynamic filtering was used to identify criteria for removing assembly artifacts. Trackster provides a general framework for running tools and dynamically filtering data. Many other Galaxy tools can be run in Trackster, including genomic operations tools (intersect, subtract) and SNP finding tools. Dynamic filtering is available for many different data types, including BED, GFF/GTF, and BAM. Visualizations embedded in this page demonstrate how Trackster can be used for collaborative analysis. All shared, published, and embedded visualizations are fully functional. All Trackster functionality requires only a Web browser to use.