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Thread: Dante Labs Long Read Test

  1. #41
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    Quote Originally Posted by Petr View Post
    My kit was delivered to Italy on April 26th and the status is "Waiting confirmation from Dante Labs" too.

    My previous kits delivered to Dante on March 8th were marked as "Kit received" on April 2nd. In the past, it took just few days to see "Kit Delivered" and then 2-3 weeks to see "Successful DNA extraction - Level A".

    The situation look much worse now.
    Well 'Mark' on the help desk seems to have been replaced with 'Shanece'. I emailed them once already about the same issue, first of all she got it jumbled up with my earlier WGS kit even though I was very clear, then when she realised which one I meant she simply informed me that its status said 'Waiting for confirmation' and when that status changed they would email me.

    I've just had another go!
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    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
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  2. #42
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    Ireland England Netherlands Germany France
    My Long Read kit was marked received on Monday. Three weeks after I dropped the sample in the mail to return to the Utah collection site.

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  4. #43
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    And today my long read kit jumped from "Waiting for confirmation" to "Success DNA - A"
    Looks like I was wrong, and the problem is more with their IT system, considering they are also not sending out any more email notifications..

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  6. #44
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    Astonishing!

    In fact its double astonishing as so has mine, but I've been bombarding their help desk the last couple of days about updating my status...
    Last edited by MacUalraig; 05-14-2019 at 06:53 PM.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    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
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  8. #45
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    Newsflash - a 93Gb FASTQ file link has appeared attached to my nanopore kit!
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    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
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  10. #46
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    Quote Originally Posted by MacUalraig View Post
    Newsflash - a 93Gb FASTQ file link has appeared attached to my nanopore kit!
    That would have been fast results then Can you check whether the reads in the FASTQ file are really long reads?

  11. #47
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    Indeed, I take everything back about their lab not being ready (Edit: they were really fast and sequenced just 10days after the sample arrived, the fastq shows the exact time/date)
    My own long reads fastq.gz is 138GB and will be downloading for a while...
    Some preliminary stats gathered from the first 6% (8GB compressed, 16GB unzipped) of the file:
    Longest Read: 192013 bp
    Median Read: 2616 bp
    Average Read 5765 bp
    N50>13923bp (50% of all data is contained in reads longer than ~14k bp)
    read quality: median phred score: ~14
    predicted coverage: ~45x 3.2Gbp

    I have no idea how homogeneous the data will be, so these numbers could change completely once I have the downloaded the remaining 94%.

    And of course, looking at their website, it's a bit difficult to tell how much they promised in terms of N50 length
    cap.png
    Last edited by pinoqio; 05-17-2019 at 09:14 PM.

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  13. #48
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    Mine took about 3h to download on my recently upgraded broadband but I've got to transfer it then run some analysis so probably leave that running overnight now. Please keep the reports coming!
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    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
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  15. #49
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    Quote Originally Posted by pinoqio View Post
    And of course, looking at their website, it's a bit difficult to tell how much they promised in terms of N50 length
    cap.png
    As discussed previously, it's not certain if that's what they actually mean, but it's extremely clear what that is saying: Majority of reads in a sample are over 8,000 basepairs, with an average of over 20,000 basepairs between samples. Of course, that's indeed not a promise. Although since the molecule has to pass through the pore before it can be outputted, I suspect the beginning of the FASTQ's would have the shortest reads, and with the pores getting stuck in the end, read length starting to slowly fall again towards the end. (That is assuming they've not been re-ordered, of course).

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  17. #50
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    Quote Originally Posted by pinoqio View Post
    Indeed, I take everything back about their lab not being ready (Edit: they were really fast and sequenced just 10days after the sample arrived, the fastq shows the exact time/date)
    My own long reads fastq.gz is 138GB and will be downloading for a while...
    Some preliminary stats gathered from the first 6% (8GB compressed, 16GB unzipped) of the file:
    Longest Read: 192013 bp
    Median Read: 2616 bp
    Average Read 5765 bp
    N50>13923bp (50% of all data is contained in reads longer than ~14k bp)
    read quality: median phred score: ~14
    predicted coverage: ~45x 3.2Gbp

    I have no idea how homogeneous the data will be, so these numbers could change completely once I have the downloaded the remaining 94%.

    And of course, looking at their website, it's a bit difficult to tell how much they promised in terms of N50 length
    cap.png
    Longest read 275622
    N50 21174bp

    I have a fastqc running too will post that when it finishes. Then will have a look at some aligning. Might try this one:

    https://github.com/lh3/minimap2

    Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome;
    Last edited by MacUalraig; 05-18-2019 at 11:47 AM. Reason: n50 recalc
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    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

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