Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • why does Cufflink does not report strand information for unspliced reads

    Hi there,

    I have been using cufflink to predict transcript, but cufflink does not provide strand info on it. Could someone please suggest me how to solve that.
    This is how i run the program

    # Mapping of reads by tophat
    tophat --num-threads 7 --solexa-quals --output-dir Transcript_Mapped/Eggs --butterfly-search /export/data/alignment_references/bowtie/danRer7 Raw_Reads/Eggs_fastq


    # Construction of trasncripts
    cufflinks --output-dir Eggs/ --num-threads 4 --frag-bias-correct /export/data/alignment_references/bowtie/danRer7.fa --multi-read-correct --upper-quartile-norm /home/chirag/Projects/danRer7_RNASeq/Project_FM009/Transcript_Mapped/Eggs/accepted_hits.bam

    # Merge transcripts
    cuffmerge --num-threads 6 -s /export/data/alignment_references/bowtie/danRer7.fa -o Version-1 assemblies.txt



    Transcript.gtf and Merge.gtf is now covered into .bed

    chr1 1906 4188 CUFF.1.1 1000 . 0 0 0 1 2282, 0,
    chr1 39115 39565 CUFF.2.1 1000 . 0 0 0 1 450, 0,
    chr1 39666 39981 CUFF.3.1 1000 . 0 0 0 1 315, 0,
    chr1 1 745 CUFF.4.1 1000 . 0 0 0 1 744, 0,
    chr1 36295 36812 CUFF.5.1 1000 . 0 0 0 1 517, 0,
    chr1 4343 35664 CUFF.6.1 1000 - 0 0 0 4 829,86,65,858, 0,6063,6921,30463,
    chr1 4343 27499 CUFF.6.2 1000 - 0 0 0 4 829,86,65,837, 0,6063,6921,22319,


    We can see when the transcript is unspliced, it is unable to predict the strand.
    Even if i look at the GTf file, there is no strand information.


    The RNASeq data i used is 76 bp long, from Illumina, and has not strand information.
    As far as i am aware, Cufflink should be able to predict the strand irrespective of the strand specific RNASeq data. I guess, it is not because of low coverage, since we have around 250 million reads per sample.

    Could you please suggest me on this, how can this be solved ?
    Is there any parameters which i have missed while making the transcripts ?

    Thanks for your help in advance !

    regards
    Chirag

  • #2
    How do you think cufflinks predicts the strand information if it is not in the data?

    Of course it does not have magic omniscience. Rather, it looks at splice sites to infer the strand. (The splice donor on the 5' side of an intron is (nearly) always GU, the splice acceptor on the 3' side is AG.) If there is no intron, this will not work.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-27-2024, 06:37 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X