合并基因表达水平(merge gene expression levels, FPKM)

使用tophat和cufflinks计算RNA-seq数据的表达水平时，当一个基因在一个样本中有多个表达水平时需要合并它们的表达水平。

 

This code is a solution to collapsing duplicate FPKMs for a gene.

CollapseFPKM

This code is a solution to collapsing duplicate FPKMs for a gene

Problem/Issue:

In the cufflinks output files *_genes.expr (which reports the gene-level coordinates and expression values), sometimes I get more than one row for the same gene? It's like in some cases the FPKM values from the transcripts corresponding to the same gene do not get summed, although the transcripts are assigned to the same gene.

 

Reasons and Solution:

The multiple FPKM problem occurs when genes have transcripts that do not overlap with any other transcripts in the gene. For example, this occurs in the ENSG00000125388 gene from ENSEMBL/hg19. We are aware of this issue and will eventually change the behavior, but for now a simple solution is just to sum the FPKMs since the gene FPKMs are just the sum of the transcript FPKMs anyways.

 

网址：

https://sourceforge.net/projects/collapsefpkm/files/?source=navbar