Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • StevenW
    replied
    Hi,

    I am based in the Forum. Today is fine to discuss (morning is better).

    S

    Leave a comment:


  • dawe
    replied
    Originally posted by StevenW View Post
    Hi,

    I’m a bioinformatician at the Babraham Institute in Cambridge, UK and I’ve just produced a pipeline (named HiCUP) for processing Hi-C sequence data.
    Whoa! That's pretty interesting. I'm at Brabaham for EagleGenomics Symposium today... do you think we can meet and chat about it?

    d

    Leave a comment:


  • colindaven
    replied
    For those who also didn't know what this is :

    "
    Hi-C, developed from 3C, identifies long-range genomic interactions. The Hi-C protocol involves formaldehyde-fixing cells to create DNA-protein bonds that cross-link interacting DNA loci. The DNA is then digested and ligated to generate a library of products that were spatially close to each other in the nucleus.
    "

    Leave a comment:


  • StevenW
    started a topic Hi-C User Pipeline (HiCUP)

    Hi-C User Pipeline (HiCUP)

    Hi,

    I’m a bioinformatician at the Babraham Institute in Cambridge, UK and I’ve just produced a pipeline (named HiCUP) for processing Hi-C sequence data.

    The pipeline, comprising several Perl scripts, receives FASTQ data which is then de-multiplexed (if required), mapped against a reference genome and filtered to remove frequently encountered experimental artefacts. The pipeline produces paired read files in SAM/BAM format, each read pair corresponding to a putative Hi-C di-tag.

    Although the pipeline should be considered a work-in-progress (we expect to add more functionality and modify various components of the pipeline, such as how HiCUP classifies putative Hi-C artefacts), it has been used successfully by us when analysing Hi-C data.

    We would welcome any thoughts you may have on HiCUP, whether they concern its strengths, weaknesses, how it could be improved or future augmentations.

    The project’s homepage is: http://www.bioinformatics.babraham.ac.uk/projects/hicup

    I look forward to hearing from you and contributing to the Next-Generation Sequencing Community.

    Kindest regards,
    Steven Wingett

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Working...
X