Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cuffcompare Result help

    Dear all,

    I just run cuffcompare -r [reference.GTF] [transcript.GTF], the output file included the transcripts.tmap which showed gene names and FPKM info. Following is one of the genes:

    Bdnf ENSMUST00000053317 = CUFF.114250 CUFF.114250.1 97 32.073177 28.162251 35.984103 35.033306 1633 CUFF.114250.1
    Bdnf ENSMUST00000111050 = CUFF.114251 CUFF.114251.2 100 33.063804 27.584704 38.542903 36.115361 1249 CUFF.114250.1
    Bdnf ENSMUST00000111052 = CUFF.114252 CUFF.114252.3 62 20.483324 14.448689 26.517959 22.373791 1105 CUFF.114250.1
    Bdnf ENSMUST00000111047 c CUFF.114254 CUFF.114254.1 100 10.649808 7.099872 14.199745 11.639716 235 CUFF.114254.1
    Bdnf ENSMUST00000111042 c CUFF.114256 CUFF.114256.1 100 23.582192 21.902030 25.262353 25.777043 2323 CUFF.114256.1
    Bdnf ENSMUST00000053317 p CUFF.114258 CUFF.114258.1 100 0.557202 0.000000 1.467470 0.609143 187 CUFF.114258.1

    I am a bit confused with the result, since I have done qPCR experiment of BDNF gene, and it will be upregulated like 5-6 folds compared with control. I only run with the treated sample and the reference GTF file, so the FPKM value is not the like fold change, right? also the class code, should I only trust "="? and what does "p" and "i" mean? If I only use "=" FPKM value, how can I extract the one with the class code "="?

    And if I run cuffcompare -r [reference.GTF] [treated.GTF] [control.GTF], how could I get the fold changes (treated/control)?

    Sorry for such naive questions? Can someone kindly explain to me?

    With many thanks in advance!!

    Wei

Latest Articles

Collapse

  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    Yesterday, 01:16 PM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 07:15 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 10:28 AM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 07:35 AM
0 responses
20 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Working...
X