Do you want to consider upgrading your python scripts?

[wlwtan]

Hi,

I find it very hard to execute your scripts.
Are you working on any packages that allow us to do cf-nucleosome analysis?
Thank you.

[mwsnyder]

Hello wlwtan, Thanks for your interest in our work. I am sorry to hear that you are having difficulty executing our scripts. I know that several of the datasets and software packages that we used at the time have since been updated to newer versions, and I would strongly recommend that you consider using updated datasets from Human Protein Atlas or GTEx (among others) if you are considering studying nucleosome footprints in cfDNA. At this time, we have no plans to upgrade our python or R scripts. Best regards, Matthew Snyder

…

On Mon, Jul 27, 2020 at 6:39 AM wlwtan ***@***.***> wrote: Hi, I find it very hard to execute your scripts. Are you working on any packages that allow us to do cf-nucleosome analysis? Thank you. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABN4KBAYXCFPI35GZVX7KNTR5V7QRANCNFSM4PIY274A> .

[wlwtan]

Dear Synder, Thanks for your prompt response. I have generated my own pilot datasets and was hoping to be able to use your algorithms to look for cell free nucleosome signature, and subsequently infer the cell type origin. To be specific, im stuck at the stage of nucleosome calling. Specific questions: how do you decide the region to look at for nucleosome signatures? TSS? Or is there an updated unbiased way of doing that? Have you tried if usual peak calling algo would work? Thank you. Get Outlook for Android<https://aka.ms/ghei36>

________________________________ From: Matthew Snyder <notifications@github.com> Sent: Tuesday, July 28, 2020 2:38:12 AM To: shendurelab/cfDNA <cfDNA@noreply.github.com> Cc: TAN Lek Wen Wilson <wlwtan@gis.a-star.edu.sg>; Author <author@noreply.github.com> Subject: Re: [shendurelab/cfDNA] Do you want to consider upgrading your python scripts? (#6) Hello wlwtan, Thanks for your interest in our work. I am sorry to hear that you are having difficulty executing our scripts. I know that several of the datasets and software packages that we used at the time have since been updated to newer versions, and I would strongly recommend that you consider using updated datasets from Human Protein Atlas or GTEx (among others) if you are considering studying nucleosome footprints in cfDNA. At this time, we have no plans to upgrade our python or R scripts. Best regards, Matthew Snyder

On Mon, Jul 27, 2020 at 6:39 AM wlwtan ***@***.***> wrote: Hi, I find it very hard to execute your scripts. Are you working on any packages that allow us to do cf-nucleosome analysis? Thank you. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABN4KBAYXCFPI35GZVX7KNTR5V7QRANCNFSM4PIY274A> .

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[wlwtan]

Thank you, I have resolved this.

[feihongloveworld]

Thank you, I have resolved this.

hi sir：
do you have any faster method to call wps of deep wgs data ？

[makirc]

No, not at this point.