Hello all,
I am trying to output the count table that is created to be used for differential expression analysis in DESeq. I'm just having trouble on what code to use to get a tab-delimited text file with Gene_ID as row headers and replicates as column headers.
This is what I have so far. Could this be done in HTSeq-count?
I am planning on using this count table with a tool called Scotty - "a tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims" Check it out here: http://scotty.genetics.utah.edu/
Thanks
I am trying to output the count table that is created to be used for differential expression analysis in DESeq. I'm just having trouble on what code to use to get a tab-delimited text file with Gene_ID as row headers and replicates as column headers.
This is what I have so far. Could this be done in HTSeq-count?
Code:
library("DESeq2") files = c("merged_sample_2.bam_htseq_out.txt","merged_sample_11.bam_htseq_out.txt","merged_sample_20.bam_htseq_out.txt","merged_sample_3.bam_htseq_out.txt","merged_sample_12.bam_htseq_out.txt","merged_sample_21.bam_htseq_out.txt") cond = c("GFP","GFP","GFP","DBM","DBM","DBM") sTable = data.frame(sampleName = files, fileName = files, condition = cond) dds <-DESeqDataSetFromHTSeqCount(sampleTable=sTable, directory = "/Volumes/cachannel/RNA_SEQ/Notch_RNASeq/in_silico_test/DESeq", design = ~condition)
Thanks
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