Hi Suzan,
The problem here is that there's an absence of data for one of the genes
you want to compare, so one can't really assign any significance to that
particular gene or transcript.
This would require inventing a singificance value where if a gene is
highly expressed in one sample, but not mea
Hello everyone,
I am comparing two samples (control and treated) paired end RNA Seq data.
In the cuffdiff output I have noticed that few genes have zero FPKM value
in one sample and other sample has significant FPKM value.
I want to identify uniquely expressed genes identified only in one sample
(
Hello Susan
The tool is using the identifier in the "gene_id" attribute from the
reference annotation GTF to name the output.
This link at the tool manual can help:
http://cufflinks.cbcb.umd.edu/howitworks.html#hdif
The iGenomes dataset may be what you are looking for. "Shared Data ->
Data
Hello,
I am new to using Galaxy tools. I am running paired end RNA-Seq data on
Galaxy and I want to differential gene expression between control and
treated samples
I was fine until running TopHat output, I am having problems with cufflinks
and cuffdiff output.
I ran the cufflinks and cuffdiff t
Hi,
I have ran Cuffdiff and got output files: transcript differential expression
testing, gene differential expression testing. Could you please tell me how to
get the significant differential expression gene and transcript ?
Thanks,
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