brent pedersen

@brent_p

computational biologist with Quinlan Lab at UU

Salt Lake City, UT
Vrijeme pridruživanja: listopad 2008.

Tweetovi

Blokirali ste korisnika/cu @brent_p

Jeste li sigurni da želite vidjeti te tweetove? Time nećete deblokirati korisnika/cu @brent_p

  1. proslijedio/la je Tweet
    prije 11 sati

    Introducing "Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED" with et al. Does selective enrichment and depletion of any targeted genomic region purely in software for sequencing.

    Prikaži ovu nit
    Poništi
  2. proslijedio/la je Tweet
    31. sij
    Odgovor korisniku/ci

    MMRF CoMMpass has ~1000 shallow genomes, exomes and RNA-Seq. The cells are sorted and hence are high purity.

    Poništi
  3. proslijedio/la je Tweet
    29. sij
    Odgovor korisnicima

    Geuvadis is basically rna-seq from 465 1kg samples

    Poništi
  4. 29. sij

    what is the largest set of broadly usable (including dbgap, ICGC) human samples for which there is both WGS and RNA-Seq?

    Poništi
  5. proslijedio/la je Tweet
    29. sij
    Odgovor korisniku/ci

    I like Cranefoot for drawing pedigrees.

    Poništi
  6. 28. sij
    Prikaži ovu nit
    Poništi
  7. 28. sij

    somalier helps to find sample swaps. it was still difficult to rectify bad information. as of pending release, it will infer pedigree structure for first-degree relatives (which can extend to large pedigrees) can infer sibs without parents present and can join families.

    Prikaži ovu nit
    Poništi
  8. 28. sij

    super-pedigree. drawn with 's awk -> dot 1-liner

    Poništi
  9. 28. sij
    Prikaži ovu nit
    Poništi
  10. proslijedio/la je Tweet
    28. sij
    Odgovor korisnicima

    Just for your information: one-linear using Graphviz (no web interface) for pedigree drawing: awk -v family=1 'BEGIN{print "digraph fam{"} family==1{if($3!="0"){printf("%s -> %s;\n",$3,$2)}if($4!="0"){printf("%s -> %s;\n",$4,$2)}} END{print "}"}' test.ped | dot -Tpng -o fam.png

    Poništi
  11. 28. sij

    wanted: an online tool where one can paste a pedigree/fam file and get a pedigree drawing.

    Prikaži ovu nit
    Poništi
  12. proslijedio/la je Tweet
    27. sij

    HG002 data release from . HiFi, CLR, PromethION, GridION, Hi-C, Strand-seq, opmaps... CC0-licensed. Benchmarking to inform production sequencing recipe

    Poništi
  13. proslijedio/la je Tweet
    21. sij

    Asking 400 students to send me cell biology memes may be my best idea of 2020.

    Prikaži ovu nit
    Poništi
  14. 17. sij

    percent of non-PASS variants from GATK is much higher on chrX . is this widely known? ?

    Poništi
  15. proslijedio/la je Tweet
    16. sij
    Prikaži ovu nit
    Poništi
  16. proslijedio/la je Tweet
    16. sij

    currently testing a new nextflow script for a few bams using 's somalier . "fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs"

    Prikaži ovu nit
    Poništi
  17. proslijedio/la je Tweet
    16. sij

    Finally managed to get URMAP running from start to finish. The good news: it does align reads fast. The bad news: it appears to be in an alpha state lacking core features necessary to really evaluate its impact on downstream analyses. (1/n)

    Prikaži ovu nit
    Poništi
  18. 16. sij
    Prikaži ovu nit
    Poništi
  19. 16. sij

    I am sympathetic to those trying to make non-commercial software licenses work, but am seeing this. Does this seem unusable to anyone else?

    Prikaži ovu nit
    Poništi
  20. 16. sij

    d-PBWT: dynamic positional Burrows-Wheeler transform

    Poništi

Čini se da učitavanje traje već neko vrijeme.

Twitter je možda preopterećen ili ima kratkotrajnih poteškoća u radu. Pokušajte ponovno ili potražite dodatne informacije u odjeljku Status Twittera.

    Možda bi vam se svidjelo i ovo:

    ·