search

cangermueller / deepcpg

Deep neural networks for predicting CpG methylation
MIT License
143 stars 66 forks source link

CpG sites in the negative strand #33

Open yasin-chop opened 4 years ago

yasin-chop commented 4 years ago

When I trun dcpg_data.py it gives thousands of warnings "dcpg_data.py:152: UserWarning: No CpG site at position 47655381! "

I think the reason is that those CpG sites are on the negative strand. Is there a solution for this?

cangermueller commented 4 years ago

You have to make sure that CpG position in the input file point to the C of CG sites in the genome. dcpg_data does not align positions automatically. You have to take care of this. Maybe your positions are shifted by +1 or -1.

On Mon, Sep 30, 2019 at 7:40 AM yasin-chop notifications@github.com wrote:

When I trun dcpg_data.py it gives thousands of warnings "dcpg_data.py:152: UserWarning: No CpG site at position 47655381! "

I think the reason is that those CpG sites are on the negative strand. Is there a solution for this?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cangermueller/deepcpg/issues/33?email_source=notifications&email_token=ABEVZM4IFKBFT46YGRXLTW3QMIFXJA5CNFSM4I334BHKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HOSKE6A, or mute the thread https://github.com/notifications/unsubscribe-auth/ABEVZMYUMAZUMFUG45VQ5XDQMIFXJANCNFSM4I334BHA .

-- Christof Angermueller cangermueller@gmail.com https://cangermueller.com

yasin-chop commented 4 years ago

Thank you very much. I will check in detail.

Kind regards, Yasin Uzun, PhD Children's Hospital of Philadelphia

From: Christof Angermueller notifications@github.com Sent: Tuesday, October 1, 2019 12:52 AM To: cangermueller/deepcpg Cc: Uzun, Yasin; Author Subject: [External] Re: [cangermueller/deepcpg] CpG sites in the negative strand (#33)

You have to make sure that CpG position in the input file point to the C of CG sites in the genome. dcpg_data does not align positions automatically. You have to take care of this. Maybe your positions are shifted by +1 or -1.

On Mon, Sep 30, 2019 at 7:40 AM yasin-chop notifications@github.com wrote:

When I trun dcpg_data.py it gives thousands of warnings "dcpg_data.py:152: UserWarning: No CpG site at position 47655381! "

I think the reason is that those CpG sites are on the negative strand. Is there a solution for this?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cangermueller/deepcpg/issues/33?email_source=notifications&email_token=ABEVZM4IFKBFT46YGRXLTW3QMIFXJA5CNFSM4I334BHKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HOSKE6A, or mute the thread https://github.com/notifications/unsubscribe-auth/ABEVZMYUMAZUMFUG45VQ5XDQMIFXJANCNFSM4I334BHA .

-- Christof Angermueller cangermueller@gmail.com https://cangermueller.com

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/cangermueller/deepcpg/issues/33?email_source=notifications&email_token=AE7FMWYSXWPLVK7IO3L74IDQMLJSRA5CNFSM4I334BHKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD776EHA#issuecomment-536863260, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AE7FMWZNZLY3244MHOXIKATQMLJSRANCNFSM4I334BHA.

This email originated from an EXTERNAL sender to CHOP. Proceed with caution when replying, opening attachments, or clicking links. Do not disclose your CHOP credentials, employee information, or protected health information to a potential hacker.

yasin-chop commented 4 years ago

Thank you again. Model zoo links seem broken. Are you able to make them accessible?

Kind regards, Yasin Uzun, PhD Children's Hospital of Philadelphia

From: Uzun, Yasin Sent: Tuesday, October 1, 2019 3:59 PM To: cangermueller/deepcpg Subject: Re: [External] Re: [cangermueller/deepcpg] CpG sites in the negative strand (#33)

Thank you very much. I will check in detail.

Kind regards, Yasin Uzun, PhD Children's Hospital of Philadelphia

From: Christof Angermueller notifications@github.com Sent: Tuesday, October 1, 2019 12:52 AM To: cangermueller/deepcpg Cc: Uzun, Yasin; Author Subject: [External] Re: [cangermueller/deepcpg] CpG sites in the negative strand (#33)

You have to make sure that CpG position in the input file point to the C of CG sites in the genome. dcpg_data does not align positions automatically. You have to take care of this. Maybe your positions are shifted by +1 or -1.

On Mon, Sep 30, 2019 at 7:40 AM yasin-chop notifications@github.com wrote:

When I trun dcpg_data.py it gives thousands of warnings "dcpg_data.py:152: UserWarning: No CpG site at position 47655381! "

I think the reason is that those CpG sites are on the negative strand. Is there a solution for this?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cangermueller/deepcpg/issues/33?email_source=notifications&email_token=ABEVZM4IFKBFT46YGRXLTW3QMIFXJA5CNFSM4I334BHKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HOSKE6A, or mute the thread https://github.com/notifications/unsubscribe-auth/ABEVZMYUMAZUMFUG45VQ5XDQMIFXJANCNFSM4I334BHA .

-- Christof Angermueller cangermueller@gmail.com https://cangermueller.com

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/cangermueller/deepcpg/issues/33?email_source=notifications&email_token=AE7FMWYSXWPLVK7IO3L74IDQMLJSRA5CNFSM4I334BHKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD776EHA#issuecomment-536863260, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AE7FMWZNZLY3244MHOXIKATQMLJSRANCNFSM4I334BHA.

This email originated from an EXTERNAL sender to CHOP. Proceed with caution when replying, opening attachments, or clicking links. Do not disclose your CHOP credentials, employee information, or protected health information to a potential hacker.