Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Coverage around genomic feature - large amount of data

    Hi,

    I have an alignment of human data (a small bam file with less than 1M reads), and would like to calculate and plot the coverage around specific genomic features.

    Specifically, I would like to calculate coverage of 100Kbp before and after each Transcription Start Site (TSS). This can be made in windows of 1000bp. I tried different methods, mostly with R and GRanges, but couldn't get the results because of the dimension of the outputted files. The probelm is that all TSS are around 200'000, so you can imagine how gigantic the outputs are.
    An average of of the values for each window will also work (i.e. for each 1Kbp window between +100Kbp and -100Kbp around each TSS, I can plot the average of all windows with the same distance from each TSS).

    Are there any program or memory-saving methods to do this?

    Thanks in advance.

  • #2
    If you want to stick inside R, the `EnrichedHeatmap` package (which is an extension of `ComplexHeatmap` for genomics) in Bioconductor is nice for rendering the type of heatmap you're trying to make. The matrix you're generating shouldn't be too big in memory if you're on a modern machine. What's probably causing you issues is rendering the heatmap inside R. I have yet to find a good solution to this in R-- ComplexHeatmap & EnrichedHeatmap are slow. You can speed them up by rendering as raster, at the cost of a reduced quality image (see here).

    Another option is to use DeepTools plotHeatmap, but it will also take a while to render the image.

    Comment

    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
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X