Forum, Wiki and FAQ
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The Flux Forum Wiki contains the steadily growing manuals of the Flux Capacitor and Flux Simulator. There is also a comprehensive documentation of the file formats that are used in both programs and a forum dedicated to discussions about gene expresion and transcript abundance reconstruction. See below for a summary on recent posts within this forum. |  |
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Here a list of essential initial questions about RNAseq, Flux Capacitors, and everything else you always wanted to know. An extended collection of FAQ (frequently asked questions) can be found in the Wiki 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.
What is RNAseq?
RNA-Seq, also called "Whole Transcriptome Shotgun Sequencing" and dubbed "a revolutionary tool for transcriptomics", refers to the use of High-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content, a technique that is quickly becoming invaluable in the study of diseases like cancer. Thanks to the deep coverage and base level resolution provided by next-generation sequencing instruments, RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions. A comprenhensive in silico simulation of all steps in an RNA-Seq experiment is provided by the FLUX SIMULATOR
How do I get a FLUX CAPACITOR?
Browsing the internet, you will come accross various attractive seeming offers, like this, or that and that. However, in practice not all of them are serious and customer compliants accumulate, referring for instance this respectively that report. Therefore, I highly recommend you to get the latest and original FLUX CAPACITOR version as indicated in the download section.
How do I use the FLUX CAPACITOR?
A continously growing collection of examples and manual pages for the FLUX CAPACITOR and the FLUX SIMULATOR is available in the Flux Wiki. There, you can also find a description of the adopted file formats.
Does the FLUX CAPACITOR work?
In contrast to the time travelling devices mentioned there, we are confident that our one works, also in awkward moments. If you have the feeling that in your case it doesn't work, please let us know via the bugtracking system.
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. Within the Flux Project, the problem of abundancy prediction has been separated from the problem of spliceform prediction by intention - 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.
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.
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. There is a growing number of programs currently available, for instance GEM (developed by Paolo Ribeca)
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 and subsequently, try to predict transcripts from the generated contigs. May the force be with you!
