1 - Introduction
2 - Download
- 1.0.1 Release notes
- 1.0.2 Release notes
- 1.0.3 Release Notes
- 1.1 Release Notes
- 1.2 Release Notes
- 1.2.1 Release Notes
3 - Getting Started
4 - The Simulation Pipeline
- 4.1 - Gene Expression
- 4.2 - Reverse Transcription
- 4.3 - Fragmentation
- 4.4 - Final Library Preparation
- 4.5 - Sequencing
5 - Example Simulations
- 5.1 RNA Hydrolysis Protocol (M.musculus)
- 5.2 Directional RNA-Seq Protocol (H.sapiens)
- 5.3 Poly-dT Priming and DNAse Digestion (S.cerevisiae)
- 5.4 Poly-dT Priming and Nebulization (A.thaliana)
- Demo - Create Fastq file
Appendix A - File Format Specifications
- .BED Mapping Locations
- .ERR Error Model
- .FASTA/FASTQ Read Sequences
- .GTF Gene Annotations
- .LIB Library Fragments
- .PAR Simulation Parameters
- .PRO Transcriptome Profile
Appendix B - Frequently Asked Questions (FAQ)
Appendix C - JIRA Issue Tracker
Appendix D - Forum
- D.1 - General Questions
- Biological replicates
- Control error model for longer reads and polyA-tales in bed alignements.
- Does the reads generated contain adaptor sequences as in real read data ?
- FPKM from PRO
- Generating a library with reads which are specific to one locus
- How do I post a new question in the forum?
- How do I reproduce a simulation?
- How many files do I need to run the Flux Simulator?
- How to cite the Flux Simulator
- how to generate paired-end read strand specific
- How to output results in a user specified directory?
- How to simulate a bad experiment?
- how to simulate the 3 primer's bias?
- I followed the paramater file and useage ,the error that java nullpointerexception occurred.
- Is it possible to force the simulation to produce reads with the exact same length?
- Is there any way to find out which exon is sequenced?
- Stil an error while preparing sequences
- Why so many reads are truncated?
- D.2 - Gene / Transcript Expression
- An error at library preparation step
- Correct gene expression profile formula
- Differential expression and alternative splicing
- Empirical expression vector as input
- Exact number of individual AS events
- flux simulator .pro file
- Generating paired-end reads longer than 100nt
- How to simulate alternative splicing?
- How to simulate reads not containing introns
- How to simulate SNP?
- NB_MOLECULES and READ_NUMBER
- Noise Within Introns
- Simulate Differential Expression (DE)
- Simulate Exon Skipping Frequencies
- Simulating RNA-Seq in different Individuals
- Using .gtf files from iGenomes: "not sorted!"
- D.3 - Library Preparation
- 5'-peak in read coverage
- Anchored primers for RT
- Error at library preparation step
- How do I modify the PCR amplification protocol?
- New error at library preparation step
- Noise while preparing library
- Source of strong bias towards 5' ends
- Understanding behaviour of the RT_MOTIF simulation parameter
- What paramters should I change if I would like to observe strong GC bias?
- What paramters should I use to create a strong positional (3') bias?
- Why do I obtain reads that are shorter than my specified READ_LENGTH in the .PAR file?
- Why no fragmentation by sonication?
- Why simulating fragment lengths obtained by hydrolysis by Weibull distributions?
- D.4 - Sequencing and Errors
- Compatibility of Mapping Files between Simulator and Capacitor
- Covered fraction of a simulated transcript
- Error simulating large number of reads
- Exact position where reads come from
- field missing, sequence preparation errors
- fix read length / indel errors
- How to creat a custom error model
- how to fix the insert size and deviation for paired-end reads?
- Missing Data in the Genome
- Oversequencing the final library
- Running time
- Strand Specific Library?
- Which bases are mutated?
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