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I am trying to figure out the cufflinks run parameters. Here are the settings I have been using (basically default)
Max Intron Length:300000
Min Isoform Fraction:0.1
Pre MRNA Fraction:0.15
Perform quartile normalization:no
Perform Bias Correction:no
Perform Multiread correction:no
use reference annotation as a guide (hg19.gtf)
Is there a resource that discusses the merits of these settings? SOme of correction options sound good but i'm really hesitant to use them without understanding the implications. I have read the manual but am looking for a more practical answer that would allow me to set them appropriately given my experimental design:
Changes over time in two immunologically-enriched populations of cells. N=3 biological replicates. I'm after differentially expressed genes and shifts in promoter/rna processing.
Max Intron Length:300000
Min Isoform Fraction:0.1
Pre MRNA Fraction:0.15
Perform quartile normalization:no
Perform Bias Correction:no
Perform Multiread correction:no
use reference annotation as a guide (hg19.gtf)
Is there a resource that discusses the merits of these settings? SOme of correction options sound good but i'm really hesitant to use them without understanding the implications. I have read the manual but am looking for a more practical answer that would allow me to set them appropriately given my experimental design:
Changes over time in two immunologically-enriched populations of cells. N=3 biological replicates. I'm after differentially expressed genes and shifts in promoter/rna processing.