Transcript quatification tools

[indugun]

Which is best tool for transcript quantification (RSEM,cufflinks or any other) ?

[AdrianP]

I am actually interested in finding out an answer to that question as well.

I am looking through this paper http://www.nature.com/nmeth/journal/...meth.1226.html talk about the ERANGE software. However, this software seems to consist of scripts that need to be modified with specific data being analysed before any work can be done. Not sure I am up to the task.

I got a genome sequenced and assembled, and a transcription sequenced, assembled and annotated. Now I need to know gene expression relative to alpha tubulin.

[chadn737]

Nobody uses ERANGE anymore. That is so 2008. It really depends on what you want to do with the data. Differential expression between conditions, isoform discovery or alternative splicing, or comparing gene expression within a sample. Know the specific goal of the research and then that will define the tool or lack thereof.

[Jeremy]

I don't think this really has an answer yet. Different tools give different sets of DE genes, but which one is more correct is not easy to find out.

[AdrianP]

Can I at least have some examples of some tools?

Really, all I got is RNA-seq from 1 sample, and within that sample I need relative expression to alpha tubulin.

[shi]

Hi AdrianP,

I don't quite understand how you can get relative expression from only 1 sample. But for the quantification, you may try featureCounts. See this post for more info about featureCounts - http://seqanswers.com/forums/showpos...21&postcount=1

Cheers,
Wei