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apply cufflinks to ENCODE RNA-Seq data
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2.3 years ago
liu4gre • 200
United States

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 ...

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Are you running Cufflinks to get FPKM value,

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

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