How can I perform expression analysis of 454 data?
Would you mind explaining a little bit more: what exactly do you need, what type of data you have, setup, software, etc.
454 cDNA data, I have contigs assembled with the 454 Assembler. I have different experimetns(say different time points) , each run in other time and different size of lanes. Now I want to compare the expression of different genes between the conditions (how many reads each contig received? normalized over the number of total reads in this condition?)
TopHat and Cufflinks are often good tools for working with RNAseq data.
In order to give a better answer, though, we're going to need more information about what your data consists of and what your goals are.
I think firs of all you need to have your contigs/isotigs annotated (to do so you can use TopHat or Cufflinks if you have a reference genome) and then analyze the expression level of all the genes you've detected in the annotation step and then check it they are differentially expressed.
I think the key point is if you have a reference genome or not.
Here are some good review papers for you to start with, that will help you find out what's possible and what's not. Also, you can make your live with these data much easier using R & Bioconductor.
Some good resources for R where mentioned here.
I also recommend R-packages DESeq and edgeR.
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