Hello everyone, my RNA-seq (conducted by the company) includes 2 pairs of samples. The RNA-seq results showed the comparison between two samples of the same pair, but not the cross comparison between the samples of 2 pairs. Is there any methods or software to compare the two samples of different pairs from the available data?
Thank you very much.
What do you mean by compare? Finding differentially expressed genes? There is plenty of software for that but you need to be moderately competent in bioinformatics. E.g.:
- edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html)
- DESeq and DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Tutorial: https://www.r-bloggers.com/tutorial-rna-seq-differential-expression-pathway-analysis-with-sailfish-deseq2-gage-and-pathview/
And how to normalize and compare different RNA-Seq data generated by different laboratories?
For example: suppose I want to compare liver cancer RNA-Seq (generated in a German lab) against a lung cancer RNA-Seq (made in England) and an ovarian cancer RNA-Seq (sequenced in Japan).
What do you suggest?
- Badges
- Science topic
- Similar topics
- Medicine
- Disease
- Infectious Diseases