Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • ldespons
    Junior Member
    • Oct 2014
    • 1

    cufflinks problem with coverage and FPKM values

    Hi !
    It's the first time I use the Cufflinks tool and I need help.
    I used the -g option (RABT assembly) to search novel genes and isoforms in a yeast annotated genome. The RNA-Seq data are Illumina 50 bp single-end oriented reads. I run Cufflinks with default parameters :
    cufflinks -g file.gff reads.fastq.sorted.bam
    The output seems correct, but I have a lot of genes with coverage=0, FPKM=0, FPKM_conf_lo=0 and FPKM_conf_hi not equal to 0 but with a very low value. I think that these genes are expressed, probably weakly expressed.
    My question is: what parameters/options should I change in the cufflinks command to obtain non-zero values of coverage and FPKM ?
    Thanks a lot for your answers.
    Laurence

Latest Articles

Collapse

  • seqadmin
    Pathogen Surveillance with Advanced Genomic Tools
    by seqadmin




    The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
    03-24-2025, 11:48 AM
  • seqadmin
    New Genomics Tools and Methods Shared at AGBT 2025
    by seqadmin


    This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

    The Headliner
    The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
    03-03-2025, 01:39 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-20-2025, 05:03 AM
0 responses
49 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-19-2025, 07:27 AM
0 responses
57 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-18-2025, 12:50 PM
0 responses
50 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-03-2025, 01:15 PM
0 responses
201 views
0 reactions
Last Post seqadmin  
Working...