Output will include all reference transcripts as well as any novel genes and
When you ran tophat and cufflinks, did you supply a GTF file of gene descriptions? If you give the
... in each primary transcript group or gene group. The results are output in FPKM tracking files in the format described here.
For more information on the FPKM_tracking format, see the file format page.
2cells_1.fastq and 2cells_2.fastq: these files are based on RNA-seq data
in units of FPKM (in fpkm_tracking files) and as read counts (in count_tracking files). ... GTF file *, A transcript annotation file in GTF/GFF format produced by cufflinks, ...
cell type: Primary Pancreatic Ductal Epithelial Cells
genes. fpkm_tracking (newly assembled genes and expression levels), transcripts.gtf.
Cufflinks, Cuffdiff and annotation RNA Sequencing.
RNA-Seq is a valuable experiment for quantifying both the types and the