Suggestions for RNA-seq quantitation?

[jjvalenz5]

Does anyone of any suggestions for RNA-seq quantitation tool using an referenced genome for illumina reads?

[klaas.vandepoele]

Please have a look at this paper 'From RNA-seq reads to differential expression results' from Oshlack et al., 2010. Also consider adding Cufflinks and Scripture to Table 1.

Klaas

[honey]

RNA-seq quantitation

Cufflink which include cuffdiff can provide you the quantitation based on RPKM. DEseq and Seqmonk can also be useful.

[jjvalenz5]

Thank you for the suggestions, I think SeqMonk is the closest thing to what I am looking for, simple and basic; however it doesnt allow me to import my own annotated genome nor does it accept fastq files. Any other suggestions, I am continuing to look at other packages.

Thanks

[liux]

My institute does not have subscription to the journal anymore. Maybe because most articles are open-access. :sigh:

a free trial does grant me access to it. but only good for 30 days.

Please have a look at this paper 'From RNA-seq reads to differential expression results' from Oshlack et al., 2010. Also consider adding Cufflinks and Scripture to Table 1.

Klaas