gene expression analysys

[pfranchini]

Hi,
I would like to know if it is available a free software (some commercial ones like CLC and SEQman do it) able to estimate gene expression from a mRNA-seq experiment using as reference to count against simple sequences without annotation. I will appreciate your help!

Thanks

P

[kmcarr]

Tophat and ERANGE. See the Software tools thread. http://seqanswers.com/forums/showthread.php?t=43

[pfranchini]

I tried TopHat but it seems to give gene expression value in RPKM only if a gff3 with known splice junction is supplied and I have not it because I am working with a non-model organism. I am looking at ERANGE but it needs the same informations of Topahat, but I am not sure because I still have to try to run it. I spoke about CLC and SEQman because I tried them and you don't necessarily need a file with known splice junctions but you can also estimate your gene expression (in RPKM for exmaple) using as reference the contigs file created "de-Novo" from short reads (because I don't have a referenfe genome for my non-model organism). Reading the manuals of CLC and SEQman, I understood that they consider each "contig" as a "gene" and count the gene expression againt them. I would like to do something like this but I am not sure I can do it wit Tophat and ERANGE, but perhaps I missed something and any help about this approach with free softwares is really welcome!

Thanks

P

[steven]

Hi,
with no reference transcriptome i would suggest Gmorse.
http://seqanswers.com/forums/showpos...68&postcount=7. It is free.
good luck,
s.