View Single Post
Old 10-02-2015, 12:05 AM   #1
Junior Member
Location: Australia

Join Date: Mar 2014
Posts: 5
Default RNA seq analysis - small number of genes

Hi all,

I am new to RNA seq analysis and want to look at the expression of a small number of genes (8) in some publicly available RNA seq datasets.

I came up with a simple method that avoids me having to align the RNA seq reads to the genome and do a full tophat/cufflinks analysis (or similar). Briefly, what I did was: Download and QC filter SRA dataset > map the reads to a multi-fasta file containing the exonic sequences for my genes of interest with bowtie2 > filter out hits with MAPQ<30 > obtain FPKM values using eXpress.

Does anyone have any thoughts on whether my method is valid or not? My main concern is that mapping reads to such a low complexity reference may artificially inflate the number of reads that map to my genes of interest and bias the FPKM values?

Thanks in advance
sparky is offline   Reply With Quote