A string indicating the path to the file "gene FPKM tracking" file (downloaded from e.g. ...
geneFPKM: genes.fpkm_tracking file; geneDiff: gene_exp.diff file; geneCount ...
Sample type, SRA
the estimated gene-level expression values in the generic FPKM Tracking Format.
Avoid these conversion by using Excel's Text Import Wizard, e.g. via File>Import.
This analysis was performed using R (ver.
'--gene-expn-file', type=argparse.FileType('r'), help='genes.fpkm_tracking file from Cufflinks').
to work with R) support auto-completion of package names so you just have to type “Iso” ... For the purpose of illustrating importing data into R let us use some cufflinks data
+ fixCufflinksAnnotationProblem=TRUE > + ) Step 1 of 5: Importing data.
My tools of choice for this pipeline are Gsnap, samtools, Cufflinks,