Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • tschauer
    replied
    Thanks for the quick reply.

    I also assumed so that these are only the "connections". In that case these graphs have to be read somewhat differently...

    Leave a comment:


  • rboettcher
    replied
    TopHat2 is designed for RNAseq and therefore splicing aware, whereas bowtie2 is designed for DNAseq and therefore cannot handle splice junctions.

    Since your RNAseq is expected to come from exons only, bowtie2 maps to the exonic regions while TopHat2 considers the introns in between as spanned by split reads or read pairs. Therefore I assume your bedgraph visualizes the spanning reads by inserting these "flat" regions in between your exons.

    Leave a comment:


  • tschauer
    started a topic bowtie2 vs. Tophat2 RNA-Seq

    bowtie2 vs. Tophat2 RNA-Seq

    Hi,

    I have PE 100 Drosophila HiSeq RNA-Seq data. I mapped the same data using Tophat2 (changed only the inner distance estimated by Cufflinks) and Bowtie2 against the genome.

    I converted the SAM file to Bedgraph file using HTSeq.

    Somehow in the case Tophat2 I see "flat" intronic coverage and in bowtie2 not (see attachment). Did anyone have similar issues?

    The read counts per gene in the exons obtained by htseq-count do not really differ. Only in a few special cases.

    Thanks,

    T.
    Attached Files

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, 07-10-2024, 07:30 AM
0 responses
30 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
202 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
212 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
194 views
0 likes
Last Post seqadmin  
Working...
X