I have fastq files (n=40) obtained by paired-end unstranded RNA-seq. I would like to analyze these files using STAR for mapping and perform the differential expression analysis between the two groups by edgeR. I plan to apply TPM for normalized count. I am wondering if RSEM is currently necessary since STAR can generate raw count data per gene. I would be grateful if you could enlighten me.
2 answers
A complete example analysis is given here (using Rsubread instead of STAR): https://bioconductor.org/packages/release/workflows/vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.html
Thank you for your response. I can use the counts calculated by STAR, please give me a rationale why using the Rsubreade algorithm is better than using the counts generated by STAR.
Thank you for your response. You are right that I can use the counts calculated by STAR, please give me a rationale why using the RSEM algorithm is better than using the counts generated by STAR. Is it reported in papers or other sources that the RSEM generated counts are more accurate than the STAR counts?
Thank you for your reply. I'll read the RSEM paper.
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