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PCA / MDS analysis useful if only small number of genes (e.g. 1-20) diff. expressed? Alex234 RNA Sequencing 3 12-10-2013 12:59 PM

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Old 10-02-2015, 12:05 AM   #1
sparky
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Location: Australia

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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
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