Page 7 of 8 FirstFirst ... 5678 LastLast
Results 61 to 70 of 72

Thread: Long Read Chromium Whole Genome Product

  1. #61
    Company Rep
    Posts
    971
    Sex
    Y-DNA (P)
    R1b U106 Z81

    Another LR batch has undergone QC and is being sequenced.
    FGC team member.

    Hidden Content

    Join our FGC google group:
    Hidden Content

    R1b-U106 google group:
    Forum for discussion of R1b-U106
    Discussion related to all products by any company will be welcome. Discussion will not be limited to FGC

    Join here:
    Hidden Content

  2. The Following 2 Users Say Thank You to FGC Corp For This Useful Post:

     MacUalraig (03-02-2019),  pmokeefe (04-16-2019)

  3. #62
    Company Rep
    Posts
    971
    Sex
    Y-DNA (P)
    R1b U106 Z81

    For those who are interested, here is a QC example for one of the LR tests:

    Screen Shot 2019-03-05 at 9.40.46 PM.png
    FGC team member.

    Hidden Content

    Join our FGC google group:
    Hidden Content

    R1b-U106 google group:
    Forum for discussion of R1b-U106
    Discussion related to all products by any company will be welcome. Discussion will not be limited to FGC

    Join here:
    Hidden Content

  4. The Following 2 Users Say Thank You to FGC Corp For This Useful Post:

     MacUalraig (03-07-2019),  pmokeefe (03-06-2019)

  5. #63
    Company Rep
    Posts
    971
    Sex
    Y-DNA (P)
    R1b U106 Z81

    Quote Originally Posted by FGC Corp View Post
    For those who are interested, here is a QC example for one of the LR tests:

    Screen Shot 2019-03-05 at 9.40.46 PM.png
    Thus far, the QC is better than in the previous batch. We're using new equipment.
    FGC team member.

    Hidden Content

    Join our FGC google group:
    Hidden Content

    R1b-U106 google group:
    Forum for discussion of R1b-U106
    Discussion related to all products by any company will be welcome. Discussion will not be limited to FGC

    Join here:
    Hidden Content

  6. The Following 2 Users Say Thank You to FGC Corp For This Useful Post:

     aaronbee2010 (04-17-2019),  JamesKane (03-08-2019)

  7. #64
    Company Rep
    Posts
    971
    Sex
    Y-DNA (P)
    R1b U106 Z81

    Results are being returned for the latest batch. Analysis is underway.
    FGC team member.

    Hidden Content

    Join our FGC google group:
    Hidden Content

    R1b-U106 google group:
    Forum for discussion of R1b-U106
    Discussion related to all products by any company will be welcome. Discussion will not be limited to FGC

    Join here:
    Hidden Content

  8. The Following 2 Users Say Thank You to FGC Corp For This Useful Post:

     MacUalraig (03-22-2019),  Nibelung (03-22-2019)

  9. #65
    Registered Users
    Posts
    1,204
    Sex
    Location
    Glasgow, Scotland
    Ethnicity
    Pictland/Deira
    mtDNA (M)
    H5r*
    Y-DNA (P)
    R1b-M222-FGC5864

    Hybrid assembly (non-human) using a combination of PacBio and Chromium 10X:

    "We first generated contigs based on PacBio sequencing libraries, which were then merged
    with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C
    chromatin interaction map, complemented by a genetic linkage map."

    10X_PacBio.png

    https://bmcgenomics.biomedcentral.co...864-019-5642-0
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

  10. The Following User Says Thank You to MacUalraig For This Useful Post:

     pmokeefe (04-16-2019)

  11. #66
    Registered Users
    Posts
    1,204
    Sex
    Location
    Glasgow, Scotland
    Ethnicity
    Pictland/Deira
    mtDNA (M)
    H5r*
    Y-DNA (P)
    R1b-M222-FGC5864

    Quote Originally Posted by FGC Corp View Post
    Results are being returned for the latest batch. Analysis is underway.
    Is there an update, you said it would take 'up to 30 days' ?
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

  12. #67
    Company Rep
    Posts
    971
    Sex
    Y-DNA (P)
    R1b U106 Z81

    Quote Originally Posted by MacUalraig View Post
    Is there an update, you said it would take 'up to 30 days' ?
    I sent you an email. The analysis of the 10x Chromium data is particularly time consuming.
    Last edited by FGC Corp; 04-22-2019 at 10:51 PM.
    FGC team member.

    Hidden Content

    Join our FGC google group:
    Hidden Content

    R1b-U106 google group:
    Forum for discussion of R1b-U106
    Discussion related to all products by any company will be welcome. Discussion will not be limited to FGC

    Join here:
    Hidden Content

  13. #68
    Registered Users
    Posts
    1,204
    Sex
    Location
    Glasgow, Scotland
    Ethnicity
    Pictland/Deira
    mtDNA (M)
    H5r*
    Y-DNA (P)
    R1b-M222-FGC5864

    Big thank you to Greg, Leon and Justin for working hard to get my 10X reports ready for this morning as I head off to the 10X Genomics User Day at the Roslin Institute near Edinburgh!

    https://www.eventbrite.com/e/10x-gen...on-59995283508

    ""Resolving Biology with 10x Genomics
    Whether you want to dissect cell-type differences, investigate the adaptive immune system, or discover copy number variation and genomic heterogeneity on a cell-by-cell basis, the Chromium System from 10x Genomics is the answer. "
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

  14. The Following 6 Users Say Thank You to MacUalraig For This Useful Post:

     FGC Corp (04-30-2019),  gotten (05-22-2019),  JamesKane (04-30-2019),  Jan_Noack (05-05-2019),  Jatt1 (04-30-2019),  pmokeefe (04-30-2019)

  15. #69
    Registered Users
    Posts
    112
    Sex

    I got the autosomal data from my last 1st cousin yesterday and processed it to get what
    is probably my final take on phased data from my LR results. I got about 90% of the
    length of the euchromatic regions covered, the rest is simply not covered by any match that
    I can coax into giving me raw data. The LR data proved invaluable, especially using the
    last cousin, who unfortunately got his sample in one week too late to get MyHeritage's
    old chip. There are still some random missing SNPs here and there, caused by blocks
    unphased by LR and/or no cousin data for those small blocks.

    One comment: the LR phasing regions are not very reliable. I also generated (usually smaller)
    phase blocks using SNPs the LR indicated were unphased as breakpoints. It was clear
    in many places that the cousin data is saying these break in correct places where the
    LR breaks are clearly missing. On the other hand, the reverse is also true in places.
    I had to trust the cousin data to decide which was better in each case. The results
    show essentially perfect phasing for all the cousins as well as random matches (in
    the phased regions of course) with very very very few misattributed SNPs.

  16. The Following 4 Users Say Thank You to dtvmcdonald For This Useful Post:

     FGC Corp (05-05-2019),  gotten (05-22-2019),  MacUalraig (05-02-2019),  pmokeefe (05-16-2019)

  17. #70
    Registered Users
    Posts
    1,204
    Sex
    Location
    Glasgow, Scotland
    Ethnicity
    Pictland/Deira
    mtDNA (M)
    H5r*
    Y-DNA (P)
    R1b-M222-FGC5864

    Got the disk with my BAM and fastqs today, the bam is around 55.2 Gb. If you view it in IGV you can use their linked read extensions features (as long as you have a recent version) to display reads linked either by the barcode (BX tag) or molecule (MI tag). I'll be reporting in more detail on my website when I've looked at it in more detail.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

  18. The Following 3 Users Say Thank You to MacUalraig For This Useful Post:

     gotten (05-22-2019),  JamesKane (05-17-2019),  pmokeefe (05-16-2019)

Page 7 of 8 FirstFirst ... 5678 LastLast

Similar Threads

  1. Replies: 3
    Last Post: 11-25-2017, 01:21 AM
  2. P312 The Big Tree and the Chromium Long Read test
    By Earl Davis in forum R1b-P312
    Replies: 0
    Last Post: 10-04-2017, 08:20 AM
  3. Replies: 15
    Last Post: 04-01-2017, 01:10 PM
  4. Replies: 0
    Last Post: 04-08-2016, 03:18 PM
  5. Family Tree DNA Product Launch: Big Y
    By Caesarea in forum General
    Replies: 184
    Last Post: 04-18-2014, 12:42 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •