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Old 06-04-2018, 09:53 PM   #1
Junior Member
Location: Melbourne

Join Date: Jun 2018
Posts: 1
Default Galaxy tool for quantifying RNAseq data

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!
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