Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • tophat parameter setting

    Dear All,

    I was using tophat to find the splicing junctions but could not find any. I used reads with 36nt in length and 50 x estimated coverage.

    my command line:

    tophat -r 128 -i 20 -I 40000 -o tophat36_200_50 gene_index read1.fastq read2.fastq .

    In the result, I can see lots of potential junctions when visualizing coverage.wig file, but there was 0 junction detected. I was wondering why? I read the tophat paper saying the island extraction using D>=300 and user can change this parameter. which is the command line option to change it? or more suggestions?

    Thanks in advance. I also attached a part of the coverage.wig file.

    Yanju

    chr5 14679 14680 8493
    chr5 14680 14681 7339
    chr5 14681 14682 6146
    chr5 14682 14683 5051
    chr5 14683 14684 3897
    chr5 14684 14685 2755
    chr5 14685 14686 1807
    chr5 14686 14687 907
    chr5 14687 14688 2
    chr5 14688 16447 0
    chr5 16447 16483 1
    chr5 16483 19963 0
    chr5 19963 19964 790
    chr5 19964 19999 791
    chr5 19999 20000 1
    chr5 20000 21797 0
    chr5 21797 21798 1
    chr5 21798 21799 2
    chr5 21799 21833 3
    chr5 21833 21834 2
    chr5 21834 21835 1
    chr5 21835 22187 0
    chr5 22187 22223 1
    chr5 22223 22248 0
    chr5 22248 22249 3
    chr5 22249 22284 4
    chr5 22284 22285 1
    chr5 22285 25435 0
    chr5 25435 25436 119
    chr5 25436 25437 1072
    chr5 25437 25438 2010
    chr5 25438 25439 2969

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 08:47 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Working...
X