Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • --coverage-search in TopHat2 returns empty junction file

    I have the following problem: When I select the option --coverage-search in TopHat2, the junction file in the output directory is empty.

    Using "--coverage-search" makes sense here, because I want to check for novel junctions in some old RNA-Seq data (36bp single-end and 38bp paired-end), so using segment-search is not a perfect option (splitting into 18bp segments will likely produce too many ambigous alignemnts).

    The junction-files are empty both whith and without using a transcriptome annotation (human).

    However, when I turn in the segmented search (by setting --segment-length to 18 or 19) together with --coverage-search, TopHat2 seems to return junctions from the coverage-search, because more junctions are returned using both options, than when only the segmented search is used.

    The current TopHat-version installed on our cluster is "TopHat v2.0.8b"

    Can anyone tell me whether this is a bug in TopHat2, or if I'm doing anything wrong?

    Morten

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
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
41 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
46 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