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Xinlitik

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Join Date: Nov 2012

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Getting isoform info from cuffdiff output

12-10-2012, 10:24 PM

Cuffdiff found a gene of interest with several isoforms differentially expressed. Is there a way that I can see the sequence of each isoform, or better yet, which exons are used? The only difference I can find is the TCONS ID for each one, but that is an internal ID, right?

Thank you
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Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by GATTACAT

Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
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Nine Things a Sample Prep Scientist Thinks About Before Sequencing

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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
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