Hello,
I am a bench developmental biologist with essentially 0 bioinformatics background, so please excuse my stupidity.
I generated 12 HTSeq count files (4 experimental conditions - 1 control experiment and 3 gene knockdowns, 3 biological replicates for each condition, single end 50 bp reads, not strand specific) from my tophat alignments. I would like to use DESeq to analyze differential gene expression in my samples. My problems start with me not understanding the explanation of how I should create a CountDataSet from my 12 files, and the pasilla example on the DESeq web page is not helping. Can someone please help me with that?
I would also be grateful for a link to a detailed step-by-step protocol for DESeq on HTSeq counts (not the one from the DESeq page - I have that already, and it is not "for dummies" enough for me).
Thanks!
Grigory
I am a bench developmental biologist with essentially 0 bioinformatics background, so please excuse my stupidity.
I generated 12 HTSeq count files (4 experimental conditions - 1 control experiment and 3 gene knockdowns, 3 biological replicates for each condition, single end 50 bp reads, not strand specific) from my tophat alignments. I would like to use DESeq to analyze differential gene expression in my samples. My problems start with me not understanding the explanation of how I should create a CountDataSet from my 12 files, and the pasilla example on the DESeq web page is not helping. Can someone please help me with that?
I would also be grateful for a link to a detailed step-by-step protocol for DESeq on HTSeq counts (not the one from the DESeq page - I have that already, and it is not "for dummies" enough for me).
Thanks!
Grigory
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