Simulating RNA-seq Reads for ASE

[sphil]

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

[Phoenix_ICE]

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.

[sphil]

Thank you!

[sphil]

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.

[dpryan]

Just make a smaller annotation including only the genes/transcripts of interest.

[sphil]

oh my god, sometimes i can just kill myself. Thank you so much...!