Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • What does cufflinks compare BAM file to, without reference?

    Hello everybody!

    Main question: with a minimal syntax like this

    cufflinks -p 3 target.bam

    what does cufflinks use to assembly the information contained in target.bam file?

    I'd also like to know whether using a local reference (the fat 16GB+ files you can download from cufflinks website) cufflinks will name the transcripts with the gene names instead of CUFF.65279 and the like.

    I'm a wet biologist trying to learn some bioinformatics. I managed to use bwa and picard to process the raw Illumina reads and get to a .bam file, and now I'm trying to learn how get some DE data out of my samples, but I hadn't found any tutorial clear enough to explain what cufflinks is actually doing. This is also why my thoughts are hazy and my questions are -probably- not outstanding.

    Thank you for yuor help and support, as well as anyone who wrote some beautiful tutorials on SEQwiki.

  • #2
    Update: I have managed to find some aid and comfort in a nicely written tutorial. If you're a newbie (like me), you don't know very well what you are doing (like me) and you're still awed by the magic behind cufflink/cuffdiff, you should try and read these:



    especially this:

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Exploring the Dynamics of the Tumor Microenvironment
      by seqadmin




      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
      07-08-2024, 03:19 PM
    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      06-25-2024, 06:43 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 07:20 AM
    0 responses
    24 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-16-2024, 05:49 AM
    0 responses
    38 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-15-2024, 06:53 AM
    0 responses
    44 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    41 views
    0 likes
    Last Post seqadmin  
    Working...
    X