[Bioc-devel] BSgenome changes
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Tue Aug 18 19:06:32 CEST 2020
On 8/18/20 01:40, Kasper Daniel Hansen wrote:
> In light of this, could we get a version of GRCh37 with only a single
> mitochondrial genome?
You mean a BSgenome.Hsapiens.NCBI.GRCh37.p13 package? So it would
contain the same sequences as BSgenome.Hsapiens.UCSC.hg19 but without
the hg19:chrM sequence?
Certainly doable but note that by using BSgenome.Hsapiens.UCSC.hg38 you
stay away from this mess. I'm not sure that adding yet another BSgenome
package would make the situation less confusing.
>
> On Fri, Aug 14, 2020 at 6:17 PM Hervé Pagès <hpages using fredhutch.org
> <mailto:hpages using fredhutch.org>> wrote:
>
> Hi Felix,
>
> On 8/13/20 21:43, Felix Ernst wrote:
> > Hi Leonard, Hi Herve,
> >
> > I followed your conversation, since I have noticed the same
> problem. Thanks, Herve, for the explanation of the recent changes on
> hg19.
> >
> > The GRCh37.P13 report states in its last line:
> >
> > MT assembled-molecule MT Mitochondrion J01415.2
> = NC_012920.1 non-nuclear 16569 chrM
> >
> > Since the last name is called "UCSC-style-name", wouldn't that
> mean that chrM has to be renamed to MT and not chrMT?
>
> This is a mistake in the sequence report for GRCh37.p13. GRCh37.p13:MT
> is the same as hg19:chrMT, not hg19:chrM.
>
> hg19:chrM and hg19:chrMT are **not** the same sequences. The former is
> NC_001807 and has length 16571 and the latter is NC_012920.1 and has
> length 16569.
>
> Yes, seqlevelsStyle() is sorting out all this mess for you ;-)
>
> Cheers,
> H.
>
> >
> > Thanks again for the explanation.
> >
> > Cheers,
> > Felix
> >
> > -----Ursprüngliche Nachricht-----
> > Von: Bioc-devel <bioc-devel-bounces using r-project.org
> <mailto:bioc-devel-bounces using r-project.org>> Im Auftrag von Hervé Pagès
> > Gesendet: Freitag, 14. August 2020 01:08
> > An: Leonard Goldstein <goldstein.leonard using gene.com
> <mailto:goldstein.leonard using gene.com>>; bioc-devel using r-project.org
> <mailto:bioc-devel using r-project.org>
> > Cc: charlotte.soneson using fmi.ch <mailto:charlotte.soneson using fmi.ch>
> > Betreff: Re: [Bioc-devel] BSgenome changes
> >
> > Hi Leonard,
> >
> > On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
> >> Dear Bioc team,
> >>
> >> I'm following up on this recent GitHub issue
> >>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ldg21
> >>
> _SGSeq_issues_5&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg&s=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE&e=
> >. Please see the issue for more details and code examples.
> >>
> >> It looks like changes in Bioc devel result in two copies of the
> >> mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one
> named
> >> chrM like in previous package versions (length 16571) and one named
> >> chrMT (length 16569).
> >>
> >> When using seqlevelsStyle() to change chromosome names from UCSC to
> >> NCBI format, this results in new behavior -- in the past chrM was
> >> simply renamed MT, now the different sequence chrMT is used. Is
> this intended?
> >
> > Absolutely intended.
> >
> > There is a long story behind the unfortunate fate of the
> mitochondrial chromosome in hg19. I'll try to keep it short.
> >
> > When the UCSC folks released the hg19 browser more than 10 years
> ago, they based it on assembly GRCh37:
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F000001405.13&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=jWtgKVQGC-SQp6i4prhKBiD5cBh2kEc8R1gL2uPlzy0&e=
> >
> > See sequence report for GRCh37:
> >
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ncbi.nlm.nih.gov_genomes_all_GCF_000_001_405_GCF-5F000001405.13-5FGRCh37_GCF-5F000001405.13-5FGRCh37-5Fassembly-5Freport.txt&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=2mzBk6ksCERabHcDIy7tR6p1aQvFGkLM8lZNrsWrA18&e=
> >
> > For some mysterious reason GRCh37 didn't include the
> mitochondrial chromosome so the UCSC folks decided to use
> mitochondrial sequence
> > NC_001807 and called it chrM.
> >
> > However, UCSC has recently decided to base hg19 on GRCh37.p13
> instead of GRCh37. A rather surprising move after many years of hg19
> being based on the latter.
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F000001405.25_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=gxOOdwtmHjZfz-EAFblY0cm-7upZ9useI3sEgDD87o8&e=
> >
> > See sequence report for GRCh37.p13:
> >
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ncbi.nlm.nih.gov_genomes_all_GCF_000_001_405_GCF-5F000001405.25-5FGRCh37.p13_GCF-5F000001405.25-5FGRCh37.p13-5Fassembly-5Freport.txt&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=epUg7bSfwCEF_WUOPlT5hPmLXHY7V51Mau09UaQNB5o&e=
> >
> > Note that GRCh37.p13 does include the mitochondrial chromosome.
> It's called MT in the official sequence report above and chrMT in hg19.
> >
> > At the same time the UCSC folks decided to keep chrM so now hg19
> contains 2 mitochondrial sequences: chrM and chrMT. Previously it
> has only one: chrM.
> >
> > So what you see in BioC devel in BSgenome.Hsapiens.UCSC.hg19 and with
> > seqlevelsStyle(genome) is only reflecting this. In particular
> > seqlevelsStyle(genome) <- "NCBI" now does the following:
> >
> > - Rename chrMT -> MT.
> >
> > - chrM does NOT get renamed. There is no point in renaming
> this sequence because it has no equivalent in GRCh37.p13.
> >
> > Hope this helps,
> >
> > H.
> >
> >>
> >> Leonard
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >>
> >
> > --
> > Hervé Pagès
> >
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
> >
> > E-mail: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> > Phone: (206) 667-5791
> > Fax: (206) 667-1319
> >
> > _______________________________________________
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> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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>
>
> --
> Best,
> Kasper
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages using fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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