[Bioc-devel] BSgenome changes

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> Im Auftrag von Herv?

Pag?s

Gesendet: Freitag, 14. August 2020 01:08
An: Leonard Goldstein <goldstein.leonard at gene.com>;

bioc-devel at r-project.org

Cc: 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
<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

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Program in Computational Biology
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https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=g4eW0swjrNpysDJ67do3xLWcLyskjH51X5-x4kMJYDw&e=

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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