I am running the following SQL query using cummeRbund, in an attempt to look at the number of genes found in a particular sample:
mySql <- "SELECT COUNT(*) FROM (SELECT DISTINCT(gene_short_name) FROM geneData JOIN genes ON geneData.gene_id = genes.gene_id WHERE sample_name = 'Str006' AND fpkm != 0)"
When I ran a cuffdiff with Str006 vs a single normal, I get one number; however, when cuffdiff was run with Str006 vs two pooled samples, I get a higher number.
I'm using cuffmerge to create a merged.gtf of the samples before sending it to cuffdiff.
Why is this?
mySql <- "SELECT COUNT(*) FROM (SELECT DISTINCT(gene_short_name) FROM geneData JOIN genes ON geneData.gene_id = genes.gene_id WHERE sample_name = 'Str006' AND fpkm != 0)"
When I ran a cuffdiff with Str006 vs a single normal, I get one number; however, when cuffdiff was run with Str006 vs two pooled samples, I get a higher number.
I'm using cuffmerge to create a merged.gtf of the samples before sending it to cuffdiff.
Why is this?
