FAQ - Frequently Asked Questions
Forum » Flux Simulator / FAQ - Frequently Asked Questions
Number of threads: 24
Number of posts: 68
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Questions that are asked rather oftenly about the Simulator
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installing Flux-SIMULATOR on Ubuntu
 by: bogdan_mirautabogdan_mirauta
13 Apr 2012 09:40 		1  
error model for FluxSimulator
 by: ndeng (guest)
18 Mar 2012 04:22 		1  
understanding of the relative abundance value
How to know the "TRUE" transcript level abundance when simulating RNA-seq data
by: mimo (guest)
16 Feb 2012 06:16 		2 by gmichagmicha
17 Feb 2012 15:11 Jump!
Can Flux Simulator generates over 100 million of reads?
 by: ndeng (guest)
15 Feb 2012 15:32 		2 by ThassoThasso
17 Feb 2012 10:55 Jump!
How do I get fastq file from FluxSimulator
 by: sango (guest)
02 Dec 2011 18:32 		3 by sango (guest)
02 Feb 2012 22:46 Jump!
Parameter can not be recognized
 by: owomo (guest)
03 Dec 2011 14:21 		3 by owomo (guest)
07 Dec 2011 08:09 Jump!
any documentation???
getting started doc?
by: someone (guest)
23 Feb 2011 18:09 		2 by Marty McFlyMarty McFly
05 Dec 2011 12:38 Jump!
Can't copy GTF file
 by: Sohail (guest)
07 Jun 2010 18:51 		4 by Marty McFlyMarty McFly
05 Dec 2011 12:35 Jump!
Is it possible to turn off the extension of transcription beyond the TSS?
 by: Marcel (guest)
27 Jun 2011 21:02 		4 by Marty McFlyMarty McFly
05 Dec 2011 12:34 Jump!
Is it possible to simulate a strand-specific library?
New sequencing protocols allow sequencing specifically of first- or second-strand cDNAs. It would be great to be able to simulate this.
by: Joshua Dunn (guest)
13 Jul 2011 20:27 		4 by Marty McFlyMarty McFly
05 Dec 2011 12:33 Jump!
Problems generating fasta files with default error model
 by: Thomas (guest)
01 Sep 2011 11:09 		4 by Marty McFlyMarty McFly
05 Dec 2011 12:32 Jump!
GTF file is not sorted?
erors occur when it try to sort a mouse GTF file: Mus_musculus.NCBIM37.63.gtf
by: Wei (guest)
21 Sep 2011 04:14 		4 by Marty McFlyMarty McFly
05 Dec 2011 12:30 Jump!
number of reads per transcript is not proportional the transcript length
 by: wei sun (guest)
25 Sep 2011 16:05 		3 by Marty McFlyMarty McFly
05 Dec 2011 12:28 Jump!
Latest simulator gui
 by: jhyrkasjhyrkas
26 Sep 2011 00:58 		2 by gmichagmicha
30 Sep 2011 12:56 Jump!
length between pair-end reads
 by: maria (guest)
01 Aug 2011 10:08 		2 by gmichagmicha
10 Aug 2011 12:50 Jump!
reading reference annotation
problems executing annotation step
by: maria (guest)
13 Jun 2011 10:27 		4 by maria (guest)
24 Jun 2011 14:45 Jump!
TRUE RPKM/FPKM
What is the best way to calculate the true RPKM/FPKM from the simulated reads?
by: mrfoxmrfox
21 Mar 2011 17:12 		2 by gmichagmicha
16 Jun 2011 16:15 Jump!
Exceptionally high fraction of polyA reads
The set of reads I obtained using FluxSim has exceptionally high fraction of polyA reads (around 35%).
by: mrfoxmrfox
21 Mar 2011 22:23 		2 by gmichagmicha
16 Jun 2011 16:07 Jump!
Errors occur when generating FASTQ file by flux simulator
Error occus, need help!
by: Bo Li (guest)
09 Dec 2010 23:13 		2 by gmichagmicha
10 Dec 2010 07:34 Jump!
size selection problem
(seen as Issue 40)
by: gmichagmicha
07 Jun 2010 19:18 		2 by gmichagmicha
07 Jun 2010 19:19 Jump!
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