Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • IBseq
    replied
    hi robby, not sure if you sorted out but I write it anyway...

    "Maybe I do something wrong. I did the following:
    1. cufflinks -G ucsc-reference.gtf sample_n.bam (for all samples)
    2. cuffdiff ucsc-reference.gtf sample_1.bam sample_2.bam [....] sample_n.bam
    3. compare genes.expr (cufflinks) with genes.fpkm_tracking (cuffdiff)
    "

    you run cufflinks correctly, but then you need to run cuffcompare and then use the output of cuffcompare to run cuffdiff to which you will provide as well the sam/.bam files from tophat...

    hope it helps,
    ib

    Leave a comment:


  • Robby
    replied
    Thanks for the fast reply, mrfox.

    Maybe I do something wrong. I did the following:
    1. cufflinks -G ucsc-reference.gtf sample_n.bam (for all samples)
    2. cuffdiff ucsc-reference.gtf sample_1.bam sample_2.bam [....] sample_n.bam
    3. compare genes.expr (cufflinks) with genes.fpkm_tracking (cuffdiff)

    @mrfox: Which values did you compare with each other? Did you perform the same steps described above?

    Leave a comment:


  • mrfox
    replied
    Hi all, I used v9.3 now and cufflinks and cuffdiff generate consistent values.

    Leave a comment:


  • Robby
    replied
    Hi all, I use version 9.3, but I still have different FPKM values returned by cufflinks and cuffdiff. Did anybody observe similar problems? Has anybody tested, which results are more trustable?

    Please let me know, if somebody has any updates or recommendations. Thank you all.

    Leave a comment:


  • fatrabbit
    replied
    hi, I also faced the same problem by using version 9.1. I'm trying to use version 9.3 (the latest one), and to see if it still has the problem.

    In their website, they said "This release fixes several issues that affect abundance estimation and differential expression accuracy, and is strongly recommended for all users."

    If you have any updates, please let me know. Thanks.
    Last edited by fatrabbit; 01-11-2011, 01:01 PM.

    Leave a comment:


  • mrfox
    started a topic Different FPKM values of cufflinks and cuffdiff

    Different FPKM values of cufflinks and cuffdiff

    Hi all, sorry for repeatedly posting the same question. But I am still confused about the different FPKM values returned by cufflinks and cuffdiff. Did I make mistakes in one of the steps? Below is how I use the package:

    1)run cufflinks on the sam files obtained by Tophat
    2)run cuffcompare on the gtf files in last step, I used UCSC known genes as the reference. And I got the stdout.combined.gtf and the tracking files as expected.
    3)using the stdout.combined.gtf obtained in 2) as reference, I run cuffdiff on the sam files of the samples and obtained the *.diff and *.tracking files.

    However, I found that for many isoforms (from isoforms.tracking), their FPKM values from the samples usually do not match those values by cufflinks from step 1). The version I used is 0.9.2.

    Could anybody help to explain this? And, what is the reason to re-assign the reads to transcript and re-estimate abundance in cuffdiff?

    I desperately look forward to your answers. Thank you all.

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM
  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
59 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Working...
X