Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • seb567
    replied
    If you'are using "bwa sampe" for aligning, the documentation says:

    Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
    I don't know if it is the case with "bwa mem" or with "bwa aln".

    Leave a comment:


  • fznajar
    replied
    You are correct GenoMax. They are identical. Appreciate it.
    Best

    Leave a comment:


  • GenoMax
    replied
    #1 = Unless there is/are SNP's which are captured by that particular read you would not be able to tell where the read came from. I assume the sequence of the gene is otherwise identical?

    Leave a comment:


  • Deciding how many reads map to a plasmid or to a genome

    Hi all,
    I have illumina genome reads for an E. coli a collaborator is studying. The prep used had a plasmid as well. I have two questions:

    1) For the reads that match both (e.g. lacI gene), how can I tell which came from the plasmid and which came from the genome?
    2) Should I normalize by dividing on the total reads per library or only the mapped reads in a library?

    Thanks in advance...
    Last edited by fznajar; 01-09-2019, 01:44 PM.

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
23 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
198 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
209 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
191 views
0 likes
Last Post seqadmin  
Working...
X