apply cufflinks to ENCODE RNA-Seq data

Question

[liu4gre]

Dear all,

I am trying to analyze ENCODE RNA-seq data with cufflinks tool. However, it always pop up errors, like Error: this SAM file doesn't appear to be correctly sorted!. After sorted with samtools, the error changed to bgzf_check_EOF: Invalid argument. I also tried to convert BAM file to SAM file, however errors still came. Anyone has suggestion for ENCODE RNA-Seq data analysis? Maybe my way is not right?

BTW, I download BAM file from ENCODE ...

[Manvendra Singh]

Are you running Cufflinks to get FPKM value,

Its always good to download fastq files, and then follow TopHat and Cufflinks pipeline.