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Hi,
Does anyone know of a repository or a database where from RNA seq FPKM values for Refseq annotated human genes can be obtained ?
I am working with the ENCODE dataset and for the asociated longRNAs they have not provided the XS files.
According the supplementary information 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 is therefore how to analyse star alignments (BAM files without XS) with cufflinks.
Kindly help.
Does anyone know of a repository or a database where from RNA seq FPKM values for Refseq annotated human genes can be obtained ?
I am working with the ENCODE dataset and for the asociated longRNAs they have not provided the XS files.
According the supplementary information 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 is therefore how to analyse star alignments (BAM files without XS) with cufflinks.
Kindly help.