Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • one transcript many genes "chimeric"

    The problem:
    I am trying to assemble the transcriptome of Belgica the antarctic midge. Some of our assembled transcripts are much larger than they should be, and they contain multiple genes . In the ones that I have dug into in depth, these genes are adjacent on the chromosomes of the draft genome. We have no reason to believe that these are biological in origin.

    The situation:
    I am working with three lanes of RNA-Seq data from a solexa machine. We have about 35 million paired end reads (70M total). Each read is 76 bp. At the same time we have a genome assembly project that is not under my direct control. It is against this draft genome that I am attempting to assemble the transcriptome with tophat/cufflinks.

    Has anybody run into this before. I have been pulling my hair out trying to tweak the input parameters of tophat and cufflinks in order to eliminate this. I have also tried filtering my reads. I accepted sequences where 75% of the sequence had a phred score of 38 or better. Both mates had to pass in order to be included.

    I have found one or two threads on various forums and they were not very helpful. The most helpful idea anyone had was to contact the authors. I tried that, but I am not holding my breath. Their automated message (below) openly stated that they may not contact me back. nice. I really appreciate any help you guy and gals can give me.

    Dear Tophat/Cufflinks User,

    Your message has been received and will be forwarded to the appropriate project members. Due to the large numbers of e-mails we receive, a response may not be immediate. We focus first on high priority bug reports before answering general questions and sometimes do not respond to repeat bug reports when a fix is already in the works. In the meantime, please have a look at the links below, which may aid in answering your questions.

    TopHat Manual: http://tophat.cbcb.umd.edu/
    Cufflinks Manual: http://cufflinks.cbcb.umd.edu/
    SeqAnswers Forum: http://seqanswers.com/

    Regards,

    The TopHat and Cufflinks Teams
    Last edited by BugSeq; 02-13-2012, 09:32 AM. Reason: forgot to add the Cufflinks letter

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, 07-19-2024, 07:20 AM
0 responses
38 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
61 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X