Swissprot db annotate

Question

[worarado.kan]

Hello,

I wonder between genes.count.matrix and isoform count matrix from edgeR, which one should select for annotate with swissprot database?

Thank you

[lieven.sterck]

would it be possible to elaborate on your question? What data do yo have, what is your main question to answer, ...

[natasha.sernova]

A survey of best practices for RNA-seq data analysis

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728800/

DESeq vs edgeR Comparison

http://www.gettinggeneticsdone.com/2012/09/deseq-vs-edger-comparison.html

edgeR: differential expression analysis of digital gene expression data

https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

See also this post:

From bam files to isoform read counts

The rest is just theory

http://www-huber.embl.de/pub/pdf/nprot.2013.099.pdf

https://web.expasy.org/docs/swiss-prot_guideline.html

http://cbsuss05.tc.cornell.edu/doc/Trinity_Lecture2.pdf

[worarado.kan]

Thank you for your information