sequenza on hg38?

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Christoffer Flensburg

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Nov 22, 2017, 12:02:06 AM11/22/17
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Hey all,

Does sequenza support hg38? The error message "Error : assembly must be one of hg19, hg18, hg17 or hg16" seems to indicate that it doesn't.

cheers,
/Christoffer

Francesco Favero

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Nov 22, 2017, 4:28:46 PM11/22/17
to Christoffer Flensburg, Sequenza User Group
Hi Christoffer,

sequenza per-se doesn’t really deal with genome build, the problem is in the copynumber package used for the segmentation.

here you can find how to use a modified version of copynumber to enable hg38, or any other genome build:
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Christoffer Flensburg

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Nov 22, 2017, 11:48:52 PM11/22/17
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Hey Francesco,

Thanks. I replaced library(sequenza) with

library(sequenza)
library("devtools")
install_github("aroneklund/copynumber")

which makes it pass that point of the run with hg38.

cheers,
/Christoffer
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Phoebe He

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May 15, 2019, 1:45:29 PM5/15/19
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Hi Francesco,

It would be really nice if sequenza can be used for mouse genomes.  Is there a way to install copynumber for mm10 just like Christoffer did?

Thanks!
Phoebe

Christoffer Flensburg

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Oct 3, 2019, 9:59:27 PM10/3/19
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Hi again Francesco!

I am back to running some Sequenza on hg38 again, and it seems there is an issue with the modified copynumber package. :/
in sequenza.extract, I get this error for each chromosome (GC information seems to go through properly).

Processing chr1:
Error in get0(oNam, envir = ns) :
  lazy-load database '/stornext/HPCScratch/home/flensburg.c/software/R/libs/copynumber/R/copynumber.rdb' is corrupt

I reinstalled the copynumber package, but the same error. I see that the github hasn't been touched for 3 years, but maybe some changes to R (this is version 3.6.0) or sequenza (3.0.0) has affected things?
Any ideas? Or are there now other ways to run Sequenza on hg38?

cheers,
/Christoffer

On Thursday, November 23, 2017 at 8:28:46 AM UTC+11, Francesco Favero wrote:
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Shixiang Wang

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Dec 2, 2019, 1:30:21 AM12/2/19
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I have the same issue and I created a fork from v1.26.0 https://github.com/ShixiangWang/copynumber, I hope it may help.

在 2019年10月4日星期五 UTC+8上午9:59:27，Christoffer Flensburg写道：

Natalia M

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Oct 27, 2020, 4:42:33 PM10/27/20
to Sequenza User Group
Hello!
Has anyone been successful in running Sequenza with samples aligned with GRCh38 -Ensembl version-?
Thanks!
Natalie
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