FAQ
What is the FLUX CAPACITOR?
It is a computer program to predict splice form abundancies from reads of an RNAseq experiment.
Can I travel in time with the FLUX CAPACITOR?
No, not with this one. To do so, you need the device described there. The sunny side is that you neither need 1.21 Gigawatts to operate the FLUX CAPACITOR described in here, just a reference transcriptome and RNAseq reads mapped to the genome.
How do I use the FLUX CAPACITOR?
I didn't have time to write a proper manual so far, however, the program communicates with you. If you have difficulties in understanding the messages, you probably disqualified from using it in its current status. In this case, if you are still interested, fill in a bugtracker file or write me an email.
Why do I need the annotation of a reference transcriptome?
The philosophy behind the flux capacitor is to find the best interpretation of the picture drawn by the reads for the reference transcripts. By intention, the problem of abundancy prediction has been separated from the problem of spliceform prediction in order to directly assess the underlying question of "how well abundancies of RNA molecules present in an experiment can be reconstructed by short sequence reads". Obviously, short reads can also be used to improve classical gene finding strategies, and in the future combined approaches are desireable.
What do I do if I don't have a reference transcriptome for my species?
You produce a reference transcriptome by using one of your favourite ab-initio gene finders on the genomic sequence of the respective species. If you are not familiar with ab-initio gene predictor programs, you can find recent benchmarks for instance here or there. Gunnar is currently developing a gene predictor that reconstructs spliceforms AND assigns an abundancies to spliceforms. You are wellcome to use the FLUX CAPACITOR alternatively to see differences in the abundancy predictions using the spliceforms produced by his program and by the FLUX CAPACITOR, we are currently working on a benchmark. After prediction of spliceforms, use the respective transcripts as a reference transcriptome for the FLUX CAPACITOR.
What do I do if I have reference transcript sequences, but they are not aligned to the genome?
Currently, use a program that is able to perform spliced alignments. UCSC for instance uses the BLAT program which can be found here. Other examples here are ....
What can I do if I have short sequence reads, but they are not aligned to the genome?
Similar to the problem given right before. Use a short read mapper. Currently publicly free available programs are ...
What can I do if I lack a reference genome of my species for ab-initio gene prediction?
Wow -- well, you will have to try to assemble the genome, either by data available from other sources or the short sequences themselves. Use a genome assembler like , or, or (there are many more). Subsequently, try to predict transcripts from the generated contigs. May the force be with you!
