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Shaun Jackman
22.6K posts
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@sjackman

Shaun Jackman

@sjackman
I develop Cell Ranger at 10x Genomics, Homebrew, and developed ABySS for my PhD at UBC. I cook, sing, travel, see theatre, and play boardgames for fun. 🏳️‍🌈
Vancouver, Canada
sjackman.ca
Joined September 2007
501 Following
2,744 Followers
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  • Pinned
    @sjackman
    Shaun Jackman
    @sjackman
    Nov 27, 2019
    🧬 10x Genomics is hiring! My first three months at 10x have been fantastic. My colleagues are friendly and helpful. 10x is based in Pleasanton, CA. Remote work may be possible, depending on the position. Check out open positions at grnh.se/c3f537b11
    1
  • @sjackman
    Shaun Jackman
    @sjackman
    Jun 21, 2022
    Is there a tool to index a BGZIP-compressed FASTQ file and extract a range of reads, like the 1,000,000–2,000,000th reads? There's grabix, and hacks converting FASTQ to TSV and using tabix, or putting the record number in the position column of SAM and using samtools index/view.
    10
  • @sjackman
    Shaun Jackman
    @sjackman
    Feb 17, 2022
    Who's serving whom here?
    You’re unable to view this Post because this account owner limits who can view their Posts. Learn more
  • @sjackman
    Shaun Jackman
    @sjackman
    Jan 25, 2022
    *For *odd* values of k…
    @sjackman
    Shaun Jackman
    @sjackman
    Jan 24, 2022
    Replying to @pashadag
    github.com/bcgsc/abyss/bl… For even values of k, ABySS splits unitigs at palindromic (k-1)-mers to prevent both a k-mer and its reverse complement from appearing in the unitig.
  • @sjackman
    Shaun Jackman
    @sjackman
    Jan 24, 2022
    > ABySS clearly exhibits the palindrome splitting artifact, with all non- ambiguous unitigs being split and none fully-covered. It's by design and intentional that ABySS splits palindromic unitigs. ABySS ensures that each k-mer and its RC is present at most once in the unitigs.
    @pashadag
    PM @[email protected] @pashadag.bsky.social
    @pashadag
    Jan 24, 2022
    In a new paper with @amatur_r, we investigated how de Bruijn graph-based assemblers exhibit systematic mis- and under-assemblies that is inherent to unitigs. x.com/biorxiv_bioinf… 1/6
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