[Bioc-devel] BSgenome changes
Well, the presence of two mitochondrial genomes is to fix a mistake by UCSC. I can appreciate the importance of representing this mistake when you build off UCSC. But it strikes me as not actually representing the h37 version of the genome, and it seems to me that we want such a representation in the project - not everything comes through UCSC. But perhaps I have not given this sufficient thought, this is just my immediate reaction. On Tue, Aug 18, 2020 at 8:18 PM Leonard Goldstein <
goldstein.leonard at gene.com> wrote:
Thanks for the explanation Herv?. Best wishes Leonard On Tue, Aug 18, 2020 at 10:06 AM Herv? Pag?s <hpages at fredhutch.org> wrote:
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 Herv? Pag?s <hpages at fredhutch.org
<mailto:hpages at 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
>
> -----Urspr?ngliche Nachricht-----
> Von: Bioc-devel <bioc-devel-bounces at r-project.org
<mailto:bioc-devel-bounces at r-project.org>> Im Auftrag von Herv?
Pag?s
> Gesendet: Freitag, 14. August 2020 01:08
> An: Leonard Goldstein <goldstein.leonard at gene.com
<mailto:goldstein.leonard at gene.com>>; bioc-devel at r-project.org
<mailto:bioc-devel at r-project.org>
> Cc: charlotte.soneson at fmi.ch <mailto:charlotte.soneson at 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
>>
<
>>
_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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>
> --
> Herv? Pag?s
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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>
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--
Herv? Pag?s
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 at fredhutch.org <mailto:hpages at fredhutch.org>
Phone: (206) 667-5791
Fax: (206) 667-1319
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-- Best, Kasper
-- Herv? Pag?s 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 at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
Best, Kasper [[alternative HTML version deleted]]