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Old 03-16-2014, 05:30 AM   #11
rskr
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Location: Santa Fe, NM

Join Date: Oct 2010
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Quote:
Originally Posted by Zapages View Post
I used to do transcripts, but I was told specifically to never to use them again as you will get more gene isoforms information through mapping it to the genome.

Please test this out by using the BAM files that are outputted through Tophat 2 and map it with the whole genome or transcript using NCBI IGV.
Well, never do genome mapping because you'll spend more time studying pseudo genes. Now, what are you going to do?

Anyway it doesn't make sense to me that you would get isoforms via genome mapping that you wouldn't get via transcriptome mapping, furthermore why would you be looking for different isoforms when you are quantifying relative expression? Is this one of the things where you are just answering the question you want to answer?
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