Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cuffcompare - FPKM==0

    Dear All,

    I am using TopHat and Cufflinks to look at RNA seq data from 4 lanes on paired end data. After running cuffcompare, most (~95%) of my FPKM values are zero in the transcript.tmap files, even though the confidence intervals are not:

    THOC1 ENST00000261600 i CUFF.168011 CUFF.168011.0 100 0.000000 0.000000 5.524216 1.892857 112 CUFF.168011.0
    THOC1 ENST00000261600 o CUFF.168003 CUFF.168003.0 100 91.833304 63.824409 119.842199 37.700000 60 CUFF.168003.0
    THOC1 ENST00000261600 i CUFF.168014 CUFF.168014.0 100 0.000000 24.039246 43.550817 27.939560 182 CUFF.168014.0
    THOC1 ENST00000261600 i CUFF.168017 CUFF.168017.0 100 0.000000 23.307955 44.481971 27.012903 155 CUFF.168017.0
    THOC1 ENST00000261600 i CUFF.168020 CUFF.168020.0 100 0.000000 1.819694 10.605954 5.139394 165 CUFF.168020.0
    THOC1 ENST00000261600 i CUFF.168023 CUFF.168023.0 100 0.000000 34.336648 81.714214 24.000000 53 CUFF.168023.0
    THOC1 ENST00000261600 e CUFF.168026 CUFF.168026.0 100 0.000000 38.204817 87.516951 26.000000 53 CUFF.168026.0
    THOC1 ENST00000261600 e CUFF.168029 CUFF.168029.0 100 0.000000 0.000000 4.871750 1.669291 127 CUFF.168029.0
    - - u CUFF.168032 CUFF.168032.0 100 0.000000 7.537617 22.612852 12.080882 136 CUFF.168032.0
    TYMS ENST00000323250 c CUFF.168035 CUFF.168035.0 100 0.000000 3.270622 14.526530 6.625000 144 CUFF.168035.0
    TYMS ENST00000323224 c CUFF.168038 CUFF.168038.0 100 0.000000 5.665085 33.018536 8.000000 53 CUFF.168038.0
    TYMS ENST00000323250 i CUFF.168041 CUFF.168041.0 100 0.000000 9.303752 23.713787 13.656442 163 CUFF.168041.0
    TYMS ENST00000323250 i CUFF.168044 CUFF.168044.0 100 0.000000 1.294351 12.812750 5.834862 109 CUFF.168044.0
    TYMS ENST00000323250 i CUFF.168047 CUFF.168047.0 100 0.000000 8.012186 23.107405 12.871429 140 CUFF.168047.0

    Cuffcompare was run like this:
    cuffcompare -o ./cuffC/100224ref -r Homo_sapiens.exon.chr.NCBI36.48_1.gtf -R tophat_Y1_100216/transcripts.gtf tophat_Y2_100215/transcripts.gtf tophat_Y3_100216/transcripts.gtf tophat_Y4_100215/transcripts.gtf

    Using cufflinks-0.8.1, tophat-1.0.12, bowtie-0.12.1. The reference GTF file was collected from ensembl and reformatted (added "chr", removed all lines except exons).

    The transcripts.gtf files all have FPKM values.

    Any idea of what could have gone wrong?

    Thank you,
    Boel

Latest Articles

Collapse

  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM
  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-28-2024, 06:12 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-23-2024, 04:11 PM
0 responses
74 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
82 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X