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Thread: Dante Labs (WGS)

  1. #721
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    I just noticed FASTQ files for download. Surprisingly, they are much smaller, last year I have received FASTQ files 40 to 52 GB each, while the new files have 19 to 24 GB each.

    I there any easy way how to determine the read length a number of reads in these FASTQ files?
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

  2. #722
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    Read length = (maximum) row length, number of reads = number of rows/4. Longer reads has fewer total reads to meet same read depth. In Paired End (PE) there's two paired FASTQ files, so either count all reads or number of paired reads. Unfortunately most editors will choke on files that large (If you even have room to extract them - IF they are compressed, lack of compression would certainly explain larger size). One trick could be to interrupt the download quickly and see if an uncompresser will extract what was downloaded, then estimate total reads from the compression ratio. I think there are some large file editors you could try, but without knowing computer & OS it's impossible to even guess.

  3. #723
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    Quote Originally Posted by Petr View Post
    I just noticed FASTQ files for download. Surprisingly, they are much smaller, last year I have received FASTQ files 40 to 52 GB each, while the new files have 19 to 24 GB each.

    I there any easy way how to determine the read length a number of reads in these FASTQ files?
    You can get statistics using FastQC, this will report read length, quality, duplicate reads, etc

    Do you have the smaller, downloadable FASTQs for the same kit that you already received on hard disk? Would be great to see a direct comparison to figure out how they are cutting down file size.

  4. #724
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    So here are the sizes of data inside my FASTQ files:

    2018, on HDD
    PS: 100 x 600184154 x 2 = 120 giga
    HB: 100 x 636133334 x 2 = 127 giga

    2019, downloaded
    OB: 150 x 342766670 x 2 = 103 giga
    BK: 150 x 417158704 x 2 = 125 giga
    JV: 150 x 312527687 x 2 = 94 giga
    HK: 150 x 302178190 x 2 = 91 giga
    MB: 150 x 358447022 x 2 = 108 giga

    FGC WGS 15x, for comparison:
    150 x 167869529 x 2 = 50 giga


    FastQC looks nice, it will take more time to get the results.

    I have no FASTQ download links for old kits.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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  6. #725
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    Quote Originally Posted by Petr View Post
    I just noticed FASTQ files for download. Surprisingly, they are much smaller, last year I have received FASTQ files 40 to 52 GB each, while the new files have 19 to 24 GB each.
    Hi Petr,
    How did you notice the FASTQ files for download? Was the URL for the FASTQ download similar to the URL for the VCF files for that kit? If so what is specific for the FASTQ URLs? I have results back for three Dante Lab kits so far. I have been able to download files (like CNV and SV) there were listed for one kit, but not another by constructing a URL by hand. Hoping that might be true for the FASTQ files too.
    YFull: YF14620 (Dante Labs 2018)

  7. #726
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    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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  9. #727
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    Quote Originally Posted by Petr View Post
    I just noticed FASTQ files for download. Surprisingly, they are much smaller, last year I have received FASTQ files 40 to 52 GB each, while the new files have 19 to 24 GB each.

    I there any easy way how to determine the read length a number of reads in these FASTQ files?
    Yeah I also have the two FASTQ files available to download:

    fastq.png

    I've downloaded and extracted the files - each one is 144 GB - total of ~300 GB:

    fastq1.PNG

    fastq2.PNG

    Question is - how can I merge them?

    Also, YFull team is awesome, and they compiled my FASTQ files into BAM file themselves !!

    Check out this update from them:

    yfull.PNG

    Next I'd like to get my BAM from them if possible, and use it to extract 23andme raw data to upload to Genesis. Maybe even send Davidski to get Global25 coordinates.
    Check out my Hidden Content
    My Y-DNA: Q-M242 -> Q-L232 -> Q-L275 -> Q-M378 -> Q-Y2016 -> Q-L245 -> Q-FGC1904 -> Q-Y2209 -> Q-Y2225 -> Q-Y2197 -> Q-Y2750 -> Q-YP1004 -> Q-YP3924;
    My mtDNA: K1a1b1a;

    My dad's mtDNA: K2a2a;

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  11. #728
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    I tried several variations of URLs modeled on the ones Petr kindly posted, but only received errors. Not clear if that was because the files don't exist or my URL attempts were incorrect (or both). It was obvious that some substrings in Petr's FASTQ URL were just the kit IDs, which I substituted for mine. But it wasn't so obvious how other random-looking substrings should be copied between the VCF URLs and the FASTQ URLs. Or maybe the random-looking substrings are different for the VCF and FASTQ URLs and this exercise is futile? Any further hints from customers who have the FASTQ downloads would be most appreciated!

    I also ordered the hard drives, but I move back and forth from America and Europe fairly frequently, so it can be hit-or-miss for me to receive a shipment.
    I just contacted a Dante Labs representative using the chat facility on their website on this topic. They replied:
    We are working in providing the download links for the raw files in each customers' account. I have forwarded your request to the relevant team for assistance.
    YFull: YF14620 (Dante Labs 2018)

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  13. #729
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    Quote Originally Posted by pmokeefe View Post
    I tried several variations of URLs modeled on the ones Petr kindly posted, but only received errors. Not clear if that was because the files don't exist or my URL attempts were incorrect (or both). It was obvious that some substrings in Petr's FASTQ URL were just the kit IDs, which I substituted for mine. But it wasn't so obvious how other random-looking substrings should be copied between the VCF URLs and the FASTQ URLs. Or maybe the random-looking substrings are different for the VCF and FASTQ URLs and this exercise is futile? Any further hints from customers who have the FASTQ downloads would be most appreciated!

    I also ordered the hard drives, but I move back and forth from America and Europe fairly frequently, so it can be hit-or-miss for me to receive a shipment.
    I just contacted a Dante Labs representative using the chat facility on their website on this topic. They replied:
    Yes I've also contacted them with a question what about my BAM file, and they promised it'll be available to download - yet no word sense (it's been two weeks).
    Check out my Hidden Content
    My Y-DNA: Q-M242 -> Q-L232 -> Q-L275 -> Q-M378 -> Q-Y2016 -> Q-L245 -> Q-FGC1904 -> Q-Y2209 -> Q-Y2225 -> Q-Y2197 -> Q-Y2750 -> Q-YP1004 -> Q-YP3924;
    My mtDNA: K1a1b1a;

    My dad's mtDNA: K2a2a;

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  15. #730
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    Quote Originally Posted by Erikl86 View Post
    Yes I've also contacted them with a question what about my BAM file, and they promised it'll be available to download - yet no word sense (it's been two weeks).
    Yesterday, I received an e-mail: "We sincerely apologize for the delay in providing your BAM files. We have nudged the relevant team for them to upload these results. You will receive a response in a few days. Please let us know if you have any other questions."

    Sounds good...

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