Refseq FPKM values for genes (hg19)

[AmitPande]

Hi,

Does anyone know of a repository or a database where from RNA seq FPKM values for Refseq annotated human genes can be obtained ?

regards,

[jwfoley]

ENCODE http://genome.ucsc.edu/ENCODE/dataMa...trixHuman.html

[AmitPande]

Thanks for the link but the problem I am facing is as follows:
I took the fastq formatted files for the polyA+ cell longRNAs and aligned them with TOPHAT.
However to take it to cufflinks I need the XS component, which I am not getting.
According the supplementary information provided by CSHL in the methods section of the UCSC genome browser ,De novo genes assembly were computed on the base of star alignments with the help of cufflinks. However, after close inspection of the corresponding sam files (generated with samtools) it turns out that the XS column is not included in the BAM alignments provided for download. According the cufflinks manual the related information is necessarily required to conduct analysis. My question therefore how to go about this matter to analyse star alignments (BAM files without XS) with cufflinks.