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Old 09-19-2013, 05:38 AM   #1
sphil
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Default Simulating RNA-seq Reads for ASE

Hey there,

i am looking for a tool / script which can simulate RNA-seq reads. The special deal about it is, that I do not need the whole run. I just need some loci simulated such that i just need reads for those loci. Any ideas?

Thanks in advance,

Phil
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Old 09-19-2013, 09:30 AM   #2
Phoenix_ICE
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RNASeqReadSimulator: A Simple RNA-Seq Read Simulator
http://alumni.cs.ucr.edu/~liw/rnaseqreadsimulator.html
RNA Seq Simulator: a part of USeq
http://useq.sourceforge.net/
FluxSimulator
http://sammeth.net/confluence/display/SIM/Home
BEERS
http://cbil.upenn.edu/BEERS/
RSEM
http://deweylab.biostat.wisc.edu/rsem/

I only used mason for genome seq simulation.
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Old 09-20-2013, 12:17 AM   #3
sphil
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Thank you!
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Old 09-24-2013, 03:37 AM   #4
sphil
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Unfortunately all of those just simulate RNA-seq reads for a whole transcriptome. What i needed is just reads simulated at specific loci, any help? Maybe I didn't see the appropriate flag or something.

Thank you.
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Old 09-24-2013, 05:26 AM   #5
dpryan
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Just make a smaller annotation including only the genes/transcripts of interest.
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Old 09-24-2013, 06:07 AM   #6
sphil
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oh my god, sometimes i can just kill myself. Thank you so much...!
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