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!
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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