Code:
isoforms.features <- features(isoforms(cuff))
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You can use this command instead:
be sure to had supplied the merged.gtf file when calling readCufflinks(). -
cummeRbund Accessing class_code
First a warm Hello to erveryone,
I've been passively reading here for a while and learnt a lot.
Now, I also have a question:
How can I access the class_code wit cummeRbund?
using
only gives "NA" for the class_code.Code:gene.features <- features(genes(cuff))
In general, I am interested in new intergenic transcripts (class_code u) and would like to access the following features:
-ID
-Location (strand, chromosome, position)
-FPKM values
-Differential expression
I have 12 sampels from unpaired Illumina RNAseq data. So far, I've followed the protocoll from Trapnell (nature 2012). After merging, I ran cuffcompare telling me there are ~260 genes with class code u. Now after running cuffdiff, I would love to know which ones are diff. expr.
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