Tophat: Is accepted_hits.sam normalized?

[jling]

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

[Cole Trapnell]

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

[jling]

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