Question: how to filter cuffdiff results by alignment count?
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gravatar for mike.thon
3.6 years ago by
mike.thon30
Spain
mike.thon30 wrote:

I have an RNA-seq dataset with three replicates from plant leaves infected with a pathogen and I would like to analyze the expression of the pathogen genes, if possible. I'm expecting the % of pathogen reads in the data set to be < 10% of the reads. I am aligning the reads to the pathogen and plant genomes separately and running cuffdiff on each genome separately.

I am examining one pathogen gene which, according to the genes.read_group_tracking file has 0 fragments in the first 2 reps and 1 fragment in the third rep. The FPKM for that third rep is 3686.97 and the FPKM in the FPKM in the gene_exp.diff file is 1228. cuffdiff reports a p-value for this gene but I ran it with the default setting for --min-alignment-count which is 10. Why is the FPKM value so high and why is cuffdiff reporting a p-value for this gene? I expect it to be excluded because it is below the --min-alignment-count threshold? Thanks

rna-seq cufflinks • 1.2k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 3.6 years ago by mike.thon30

Could you please edit your question adding the actual command that you ran?

ADD REPLYlink written 3.5 years ago by Macspider3.0k
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