Hi!

Depends on what exactly you need. You might want to take a look at these two publications:

http://www.biomedcentral.com/1471-2164/14/888

http://www.biomedcentral.com/1471-2164/14/714

If some of the things we did therein fit your requirements let me know. Then we can discuss if we can help you out.

Best,

Christian

Hi!

Unfortunately, SARUMAN will not run on a Mac or a PC, this mapper uses CUDA libraries available only under Linux. But in principle, you can use any mapper you want as long as it delivers output in BAM/SAM format. The Perl scripts were a workaround as there was no good freely available software around when we started to do this. We are currently working on putting all the needed analysis functions into our in-house visualization program called ReadExplorer (formerly VAMP) so that one does not need a degree in bioinformatics to do such analysis. Once this is done, the program will be published and made available to the community.

So if you want to use our approach/tools, you would have to wait for the release of ReadExplorer. If you need the analysis quickly, I could ask my boss of we could do the mapping and script-based stuff in-house (depends on the workload) and sent you the results for manual curation and analysis.

One big caveat: Our pipeline is fitted to the data as we produced it. To properly identify 3'-ends of novel transcripts, for example, paired-end Illumina data or an equivalent is needed.

Best,

Christian