Cuffdiff not generating the fpkm values

[mavadhani]

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