Tophat: Is accepted_hits.sam normalized?

jling

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Join Date: Oct 2009

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#1

Tophat: Is accepted_hits.sam normalized?

11-03-2009, 03:36 PM

Hi,

I was wondering how accepted_hits.sam was calculated. Is it normalized in any way?

The reason I ask is that I want to compare splicing between two samples but one of input raw sequence files is much larger than the other (e.g. a 2gb fastq file vs. a 1gb fastq) so I'm afraid that they can't be compared visually.

Thanks,
Jon
Tags: accepted_hits.sam, comparison, normalized, splicing, tophat
Cole Trapnell

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11-03-2009, 03:46 PM

They are not normalized. These are the raw alignments. You just want to compare the normalized coverage wigglegrams?
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jling

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#3

11-03-2009, 05:22 PM

Hi,

Sorry, yes, I meant the coverage.wig files. I want to visually compare them but I'm not sure if it will be accurate since the two raw sequence files are different sizes.

Are the wigglegrams normalized?

Thanks
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