Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • P-Richmond
    Member
    • Oct 2010
    • 13

    #1

    visualizing strand-specific read coverage per position

    Hello,
    I'm looking to display strand-specific RNA-seq data coverage data. I currently generate per-position strand specific coverage using genomeCoverageBed (genomeCoverageBed -ibam <in.bam>-d -s +[-]), but I wanted to see if there was a file-format where I could display both coverages in the same file. I imagine something like this:

    chr \t position \t positive_score \t negative_score
    chrI 1 0 0
    chrI 2 0 0
    chrI 3 0 0
    ...
    chrI 30299 29 11
    ...
    chrI 200399 39 2293


    or via the WIG format:
    chr = chrI; step = 1; span=1
    29 -11
    39 -2293

    for every position in the genome.

    Thanks for your help,
    Phil

Latest Articles

Collapse

  • kinpict.com
    Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by kinpict.com
    The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
    Today, 06:37 PM
  • SEQadmin2
    16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by SEQadmin2





    NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
    10-30-2026, 06:46 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 11-12-2026, 07:59 AM
0 responses
27 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-05-2026, 09:25 AM
0 responses
35 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-03-2026, 11:54 AM
2 responses
56 views
0 reactions
Last Post kinpict.com  
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
175 views
0 reactions
Last Post SEQadmin2  
Working...