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CODEX/CODEX2 for CNV detection

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Hi all,

Thanks for your interest in CODEX/CODEX2! This is the official Q&A forum for the R package CODEX/CODEX2 we developed for full-spectrum copy number variation detection by next-generation DNA sequencing. The CODEX paper is available at http://nar.oxfordjournals.org/content/early/2015/01/23/nar.gku1363.long; the CODEX2 paper is available at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1578-y.

The official website for CODEX/CODEX2 is at https://github.com/yuchaojiang/CODEX2.

If you have questions or encounter any bugs running the software, feel free to post here. We will reply as soon as I can.

Cheers,

Yuchao

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Jan 29

Pls do codeX 2.657

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Pls do codeX 2.657

Jan 29

patelk...@gmail.com, … Sarah D Weisberg3

2/15/24

Hi, I would like to use known regions how would I set the cnv_index if I have the positions (multiple

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Hi, I would like to use known regions how would I set the cnv_index if I have the positions (multiple

2/15/24

Laurent MANCHON

9/19/23

Sex of Panel of Normal samples

--Hi, for calling CNV in WES, is it possible to use a panel of normal samples with mixed sex or

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Sex of Panel of Normal samples

--Hi, for calling CNV in WES, is it possible to use a panel of normal samples with mixed sex or

9/19/23

6/6/22

CODEX2 Post-segmentation filters

Hello, In the CODEX2 tutorial, there are recommended post-segmentation filters listed at the end of

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CODEX2 Post-segmentation filters

Hello, In the CODEX2 tutorial, there are recommended post-segmentation filters listed at the end of

6/6/22

yu...@scisoon.cn, flora ponelle2

1/27/22

the problem of use codex2

Hello, I exactly have the same error, did you finally find a solution? Thanks Le lundi 27 décembre

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the problem of use codex2

Hello, I exactly have the same error, did you finally find a solution? Thanks Le lundi 27 décembre

1/27/22

Алексей Баринов

9/22/20

NAs introduced by coercion

Hello dear developers. I have moved to another virtual machine and faced problem : In segment(Y_qc,

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NAs introduced by coercion

Hello dear developers. I have moved to another virtual machine and faced problem : In segment(Y_qc,

9/22/20

Thomas Jones, Jiang, Yuchao2

8/22/20

HI Tom, I am afraid I cannot give you a direct answer for this. It's similar to the choice of

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HI Tom, I am afraid I cannot give you a direct answer for this. It's similar to the choice of

8/22/20

Thomas Jones, Jiang, Yuchao2

8/22/20

Question regarding CODEX2 results

Hi Tom, Thanks for your interest. Can you let me know how you set up the CODEX2 run? Do you have

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Question regarding CODEX2 results

Hi Tom, Thanks for your interest. Can you let me know how you set up the CODEX2 run? Do you have

8/22/20

xysj...@gmail.com, Jiang, Yuchao3

7/12/20

Installation Problem for CODEX2

Thank you very much! The R 4.0.1 works! On Friday, 3 April 2020 16:51:36 UTC-4, Jiang, Yuchao wrote:

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Installation Problem for CODEX2

Thank you very much! The R 4.0.1 works! On Friday, 3 April 2020 16:51:36 UTC-4, Jiang, Yuchao wrote:

7/12/20

Yuchao Jiang, thomasj...@googlemail.com4

7/10/20

Re: [codex_wes_cnv] Duplicated CNVs response

Ah ok, I'll be sure to do that. Thanks very much for your help! Tom On Friday, 10 July 2020 17:40

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Re: [codex_wes_cnv] Duplicated CNVs response

Ah ok, I'll be sure to do that. Thanks very much for your help! Tom On Friday, 10 July 2020 17:40

7/10/20

thomasj...@googlemail.com, Yuchao Jiang3

7/8/20

Identical CNVs residing in different chromosomes

Hi Yuchao, Depth of coverage/ associated stats appear to be fine for the majority. Below is an

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Identical CNVs residing in different chromosomes

Hi Yuchao, Depth of coverage/ associated stats appear to be fine for the majority. Below is an

7/8/20

6/27/20

Running CODEX2 more than 1 chromosome

Hello, I am a masters student at UCL and am using CODEX2 to investigate germline copy number

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Running CODEX2 more than 1 chromosome

Hello, I am a masters student at UCL and am using CODEX2 to investigate germline copy number

6/27/20

Khushbu Patel, Yuchao Jiang7

6/9/20

Error in Calculating read depth

You need to make the chromosome of the same format in your bed and in you bam files. On Jun 8, 2020,

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Error in Calculating read depth

You need to make the chromosome of the same format in your bed and in you bam files. On Jun 8, 2020,

6/9/20

5/27/20

Error while calculating read depth

Hello, I am trying to run CODEX2 on a bunch of WES bamflies (without controls). I get the following

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Error while calculating read depth

Hello, I am trying to run CODEX2 on a bunch of WES bamflies (without controls). I get the following

5/27/20

Jiang, Yuchao, vineeta singh2

3/24/20

Re: Codex2 query: norm_index

Thanks for the response. If this is normal then I guess will consider only CNV from sample 5. I have

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Re: Codex2 query: norm_index

Thanks for the response. If this is normal then I guess will consider only CNV from sample 5. I have

3/24/20

3/19/20

Using genome other than human or mouse

Hi, I am trying to use CODEX2 to detect CNVs among the genome a type of pine tree. My question is how

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Using genome other than human or mouse

Hi, I am trying to use CODEX2 to detect CNVs among the genome a type of pine tree. My question is how

3/19/20

12/8/19

Re: On running CODEX2 with 1000genomes GRCh38 WES data.

Hi, It seems something is wrong in the previous steps, eg, when you calculate the GC content etc.

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Re: On running CODEX2 with 1000genomes GRCh38 WES data.

Hi, It seems something is wrong in the previous steps, eg, when you calculate the GC content etc.

12/8/19

zhangyi, Yuchao Jiang3

9/18/19

Questions about CODEX2

mBIC is returned as one of the output values from segmentCBS. If you want to call longer CNVs, you

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Questions about CODEX2

mBIC is returned as one of the output values from segmentCBS. If you want to call longer CNVs, you

9/18/19

ramonv...@gmail.com

9/9/19

CNV visualization

Hello Yuchao, After I successfully generate the CNVs file, I'm having some trouble with IGV

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CNV visualization

Hello Yuchao, After I successfully generate the CNVs file, I'm having some trouble with IGV

9/9/19

Wipfler, Matthew, Yuchao Jiang3

8/7/19

CODEX2 - paired sample coverage

Glad that the problem was solved. Please feel free to let us know if you need further assistance.

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CODEX2 - paired sample coverage

Glad that the problem was solved. Please feel free to let us know if you need further assistance.

8/7/19

ramonv...@gmail.com, Yuchao Jiang3

7/16/19

Error in chromosome 1

Just checked the qcmat file, there is no missing values or negative results in gc line, the minimum

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Error in chromosome 1

Just checked the qcmat file, there is no missing values or negative results in gc line, the minimum

7/16/19

ramonv...@gmail.com, Yuchao Jiang2

7/12/19

Re: Segmentation without specifying negative control samples/regions

You need to write the finalcall.CBS as a table and output. Use write.table() On Jul 11, 2019, at 11:

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Re: Segmentation without specifying negative control samples/regions

You need to write the finalcall.CBS as a table and output. Use write.table() On Jul 11, 2019, at 11:

7/12/19

ramonv...@gmail.com, Yuchao Jiang5

7/8/19

Getting coverage: Error in Y[, 1:5] : subscript out of bounds

Thanks for the answers Yuchao! I was able to complete the analysis! Cheers, Ramon Em segunda-feira, 8

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Getting coverage: Error in Y[, 1:5] : subscript out of bounds

Thanks for the answers Yuchao! I was able to complete the analysis! Cheers, Ramon Em segunda-feira, 8

7/8/19

6/20/19

Hi, Thanks for your patient and I apologize for the errors you encountered — they were due to the

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Hi, Thanks for your patient and I apologize for the errors you encountered — they were due to the

6/20/19

Jiang, Yuchao, a.bha...@uliege.be3

6/19/19

Re: CODEX2 run time error

You are welcome. You may also consider combining certain regions. If you only have on average

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Re: CODEX2 run time error

You are welcome. You may also consider combining certain regions. If you only have on average

6/19/19

6/17/19

RE: [yuchaojiang/CODEX2] Error in genome[[chrtemp]] : no such sequence (#12)

Hi, You should remove chrM from the analysis. You cannot profile copy numbers from that with high

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RE: [yuchaojiang/CODEX2] Error in genome[[chrtemp]] : no such sequence (#12)

Hi, You should remove chrM from the analysis. You cannot profile copy numbers from that with high

6/17/19

5/28/19

Re: I have a question about the software "CODEX"

Hi Thanks for your interest in CODEX. CODEX/CODEX2 cannot be used for single-cell analysis. Yuchao On

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Re: I have a question about the software "CODEX"

Hi Thanks for your interest in CODEX. CODEX/CODEX2 cannot be used for single-cell analysis. Yuchao On

5/28/19

Migle Gabrielaite, Yuchao Jiang2

5/13/19

Running CODEX2 on WGS data

Hi Migle, Yes CODEX2 is primarily for WES and targeted sequencing. For WGS, I think you can start

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Running CODEX2 on WGS data

Hi Migle, Yes CODEX2 is primarily for WES and targeted sequencing. For WGS, I think you can start

5/13/19

1/19/19

Re: CODEX2 weird behavior

There's no bug. The exonic targets you have are overlapping. They should not. Yuchao ref=ranges(

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Re: CODEX2 weird behavior

There's no bug. The exonic targets you have are overlapping. They should not. Yuchao ref=ranges(

1/19/19

tiger.c...@gmail.com2

9/7/18

Multiple cohorts of tumor normal matched samples

Hi Yuchao, To make my second question more clear. What confuses me is that, when calling somatic CNVs

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Multiple cohorts of tumor normal matched samples

Hi Yuchao, To make my second question more clear. What confuses me is that, when calling somatic CNVs

9/7/18

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