Tweet
Is there an easy way to compute FPKMs from bam files (Tophat output)? I am using cuffdiff to compare 2 samples using an annotation and that gives me the FPKMs for the genes in the annotation, but is there a way to do that per sample more easily?
-
-
Hi lpn,
Cufflinks outputs the FPKM results in the first step - the cufflinks step. Here is what the manual says:"Cufflinks produces three output files:
1) transcripts.gtf ......
2) isoforms.fpkm_tracking
This file contains the estimated isoform-level expression values in the generic FPKM Tracking Format. Note, however that as there is only one sample, the "q" format is not used.
3) genes.fpkm_tracking
This file contains the estimated gene-level expression values in the generic FPKM Tracking Format. Note, however that as there is only one sample, the "q" format is not used. "
Hope this helps.
Douglas
-
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...Yesterday, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
Comment