Does anyone of any suggestions for RNA-seq quantitation tool using an referenced genome for illumina reads?
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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 -
RNA-seq quantitation
Cufflink which include cuffdiff can provide you the quantitation based on RPKM. DEseq and Seqmonk can also be useful.Comment
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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.
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