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  • Cuffdiff not generating the fpkm values

    Hello All,

    I am trying to generate a python pipeline to analyze RNASeq data. I am able to build an index of the genome, align the fastq files to the genome and get a sam output and sort the sam file. My script for running cuffdiff works fine on my personal mac. I get the fpkm values of the query files. However, when I run the exact same thing on my windows computer at work, I do get the output files, but the genes.fpkm_tracking file appears to be incomplete. There are no fpkm values instead the fields show 0. I am confused. Any help in this regard is greatly appreciated.

    Here is my script:

    # Step 6: Compare the sorted sam files using cuffdiff
    print("Comparing files")
    process = subprocess.Popen([cuffdiff, '-o/cuff_output', gffFile2, sorted_output1, sorted_output2], stdout=subprocess.PIPE)
    process.stdout.read()
    process.wait()


    Thanks,
    -M

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