Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Discovery of viral pathogen from IonTorrent data

    All,

    I'm seeking your advice and suggestions to identify the viral genome from viral-infected patient sample sequenced on IonTorrent. A totol 0.34 million reads of length 5-202bp DNA reads was generated, out of which 0.30 million reads were selected after filtering low quality reads based on read length (<20bp), quality trim (Q<14 at 5', 3') and mean QV <14.

    1) To substract the human background, the remaining reads were mapped to hg19 using Tmap, bwa, Bowtie2 using default params, provided different mapping results 45%, 10%, 12% respectively. But I see Tmap reported mapping even with say 18bp match in 200bp read, probably the reason for high mapping %. But all of them showed only 8-12% mapping with mapQ>8. What;s your opinion on this? Any other aligned I should try or any specific parameters?

    2)Next, I would like to map the unmapped reads to ~4000 viral genome db from NCBI. How can I do this as I would get the % of reads mapped to each genome and get a summary of mapping. Which tool does suite best to this?

    Anyone has any previous experience on this kind of analysis (with IonTorrent data)?

    Thanks

    Raj

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
10 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