Question: apply cufflinks to ENCODE RNA-Seq data
gravatar for liu4gre
5.4 years ago by
United States
liu4gre200 wrote:

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 ...

rna-seq cufflinks encode • 1.6k views
ADD COMMENTlink written 5.4 years ago by liu4gre200

Are you running Cufflinks to get FPKM value, 

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

ADD REPLYlink written 5.4 years ago by Manvendra Singh2.1k
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