ESME software for analysis of bisulphite sequencing traces - Where can I get the full version? (Jun/26/2009 )
I am analysing 3730 sequences traces from bisulphite-treated DNA to determine methylation. The ESME software described in Lewin et al., 2004 is apparently available for use. I downloaded the software from Epigenomics, but have been unable to analyse any traces due to them not aligning properly with the reference sequence. From a previous post on bioforum, it appears the download version is limited. I emailed Epigenomics more than a week ago, with no reply. Has anyone managed to get hold of the full version of this software, and if so, how? There are several papers referencing the original method paper, so they must have got it somehow!
Lewin, J., Schmitt, A.O., Adorjan, P., Hildmann, T. and Piepenbrock, C. (2004) Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates Bioinformatics 20: 3005-3012.
I just bought a copy of the software. It is a linux based programme, the Epigenomics AG takes some time to answer. The software is relatively expensive (about 2000 Euro). The test-software for free download only contains the chromosome 6 as a reference file. If your sequence is located somewhere else, you will not manage to get the right alignement.
Could you please tell me the commands you entered? Becvause I do not even manage to get the right commands....
THank you very much
Hi, thanks for the info.
Are you familiar with Linux? I wasn't so had to learn to get this to work! The command I used was something like:
where XXXX is the folder containing the ESME files (this may be several levels below home - you need to check the proper location first). The first part points to the esme program, while the second part points to the data folder. If you want to analyse a specific file, add the filename (e.g. data1.ab1) at the end.
Do you have the help file? It explains how the data files must be named, etc.