SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
High values of FPKM on cuffdiff Ohad Bioinformatics 14 05-09-2014 07:11 AM
Different fpkm values for cuffdiff and cuffcompare madsaan Bioinformatics 3 12-12-2012 04:14 PM
Different FPKM values of cufflinks and cuffdiff mrfox Bioinformatics 5 10-17-2012 01:10 PM
Cufflinks and cuffdiff FPKM values combiochem Bioinformatics 12 10-13-2012 11:37 PM
Cuffdiff DE significance of zero FPKM values jwalker_tgi Bioinformatics 7 10-13-2012 03:14 PM

Reply
 
Thread Tools
Old 12-13-2016, 09:35 AM   #1
mavadhani
Junior Member
 
Location: baltimore

Join Date: Jul 2016
Posts: 9
Default 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
mavadhani is offline   Reply With Quote
Reply

Tags
cuffdiff, genes.fpkm_tracking, python, rnaseq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO