comparing kallisto rsem , makind sd plot and corelation table /graph

Question

[yusuf]

Hi,

I have count table from kallisto and rsem i want to compare them , need suggestions for it.

metafile

meta

kallisto count table

txi.kallisto

rsem count table

txi.rsem

DE deseq2

dds.k

res.k

dds.r

res.r

DE edgeR

etable.k

etable.r

I don't have reference genes to normalize I am trying to make SDplot NEplot any suggestions on how should I proceed.

Answer 1

[WouterDeCoster]

A good starting point would be this workflow. Feel free to open a new question if you have a more specific question afterward.

[yusuf]

hi thank you for your comment. I hve used this manual. i have xountmatri of kallisto and rsem< also i have deseq2 and edger results from kallisto and rsem, i want to plot sd of rsem and kallisto and neplot followed by correlation plot.