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Old 03-19-2014, 02:56 AM   #16
Location: portugal

Join Date: Feb 2011
Posts: 15
Default Results of my comparison of mapping to transcriptome vs genome and DEG

So, I've finally gotten around to comparing the results of my differential gene expression analysis based on mapping to the transcriptome and genome of Arabidopsis.

I used bowtie v 1.0.0 to map to a filtered transcriptome containing only the longest gene model isoform of each gene. I have about 30 million paired end reads for each of my 4 samples (2 control, 2 treated) and roughly 45-50% of these reads mapped to the transcriptome. For the genome alignment, I used tophat v.2.0.10 and observed that 75-80% of the reads aligned.

After summarizing counts, I used DESeq 2 v1.2.10 for DEG analysis.

Similar to sazz, I didn't observe a huge difference, but one certainly exists.

What I plan on doing is using the combined information from this analysis to work with the total number of DEGs found from both analyses (1764) rather than just the intersection (1278) or the 1536 or 1506 found in the transcriptome and genome, respectively.

Can you think of any reason to object to this line of reasoning?
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