Re: [codex_wes_cnv] Duplicated CNVs response

[Yuchao Jiang]

Yes this is indeed a bit bizarre. Have you checked in your input bed file whether these correspond to the actual exons/targets?

Yuchao 

Sent from my iPhone

On Jul 8, 2020, at 4:27 AM, thomasjones1505 via CODEX/CODEX2 for CNV detection <cod...@googlegroups.com> wrote:

Hi Yuchao, 

Apologies, I accidentally deleted the previous thread. 

The coverage/associated stats appear to fine for the majority, below is an example of the results, all from different samples. I have several similar outcomes. Could it be that somewhere upstream of this positions are being matched by position only instead of chr+position?  

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Many thanks,

Tom Jones

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[thomasj...@googlemail.com]

Hi Yuchao,

Apologies but I'm not sure I fully understand. 

I think I may have resolved the issue by running CODEX separately on individual chromosomes instead of all together. But that's more of a work around rather than a real fix!

Tom

On Wednesday, 8 July 2020 11:45:23 UTC+1, Yuchao Jiang wrote:

Yes this is indeed a bit bizarre. Have you checked in your input bed file whether these correspond to the actual exons/targets?

Yuchao 

Sent from my iPhone

On Jul 8, 2020, at 4:27 AM, thomasjones1505 via CODEX/CODEX2 for CNV detection <cod...@googlegroups.com> wrote:

Hi Yuchao, 

Apologies, I accidentally deleted the previous thread. 

The coverage/associated stats appear to fine for the majority, below is an example of the results, all from different samples. I have several similar outcomes. Could it be that somewhere upstream of this positions are being matched by position only instead of chr+position?  

<Auto Generated Inline Image 1>

Many thanks,

Tom Jones

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[Yuchao Jiang]

Yes, it’s better to run each chromosome separately / in parallel. There’s an optional chr argument for CODEX2 I believe.

What I meant is to check in your input bed file whether the coordinates correspond to any row entries. But I am glad you solved this issue.

Yuchao 

On Jul 10, 2020, at 12:37 PM, thomasjones1505 via CODEX/CODEX2 for CNV detection <cod...@googlegroups.com> wrote:

Hi Yuchao,

Apologies but I'm not sure I fully understand. 

I think I may have resolved the issue by running CODEX separately on individual chromosomes instead of all together. But that's more of a work around rather than a real fix!

Tom

On Wednesday, 8 July 2020 11:45:23 UTC+1, Yuchao Jiang wrote:

Yes this is indeed a bit bizarre. Have you checked in your input bed file whether these correspond to the actual exons/targets?

Yuchao 

Sent from my iPhone

On Jul 8, 2020, at 4:27 AM, thomasjones1505 via CODEX/CODEX2 for CNV detection <cod...@googlegroups.com> wrote:

Hi Yuchao, 

Apologies, I accidentally deleted the previous thread. 

The coverage/associated stats appear to fine for the majority, below is an example of the results, all from different samples. I have several similar outcomes. Could it be that somewhere upstream of this positions are being matched by position only instead of chr+position?  

<Auto Generated Inline Image 1>

Many thanks,

Tom Jones

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<Auto Generated Inline Image 1>

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[thomasj...@googlemail.com]

Ah ok, I'll be sure to do that. 

Thanks very much for your help!

Tom 

To view this discussion on the web visit https://groups.google.com/d/msgid/codex2/e5042e20-7000-4851-a6d3-44750589b81fo%40googlegroups.com.