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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
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normalization #117

Open ghost opened 4 years ago

ghost commented 4 years ago

when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank you so much.

ghost commented 4 years ago

May I ask in function findDAR, is there any normalization being done? thanks!!

r3fang commented 4 years ago

Hi Rong,

There is no normalization down prior to the test. It starts with raw read count.

Best

On Oct 17, 2019, at 12:43 PM, rong923 notifications@github.com wrote:

when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank you so much.

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ghost commented 4 years ago

Hi Thanks so much for your reply. Is there normalization during the test? On Thu, Oct 24, 2019 at 5:35 AM Rongxin Fang notifications@github.com wrote:

Hi Rong,

There is no normalization down prior to the test. It starts with raw read count.

Best

On Oct 17, 2019, at 12:43 PM, rong923 notifications@github.com wrote:

when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank you so much.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/r3fang/SnapATAC/issues/117?email_source=notifications&email_token=ABT6GG6O2QQNWQ4P2HPPPKDQPCI4FA5CNFSM4JB4IC32YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HSQR7NA>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABT6GG64WE3VC7AF5IA7QKTQPCI4FANCNFSM4JB4IC3Q .

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r3fang commented 4 years ago

Yes! It will be normalized to CPM during the test

On Oct 24, 2019, at 12:00 PM, rong923 notifications@github.com wrote:

Hi Thanks so much for your reply. Is there normalization during the test? On Thu, Oct 24, 2019 at 5:35 AM Rongxin Fang notifications@github.com wrote:

Hi Rong,

There is no normalization down prior to the test. It starts with raw read count.

Best

On Oct 17, 2019, at 12:43 PM, rong923 notifications@github.com wrote:

when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank you so much.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/r3fang/SnapATAC/issues/117?email_source=notifications&email_token=ABT6GG6O2QQNWQ4P2HPPPKDQPCI4FA5CNFSM4JB4IC32YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HSQR7NA>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABT6GG64WE3VC7AF5IA7QKTQPCI4FANCNFSM4JB4IC3Q .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/117?email_source=notifications&email_token=AIIR2K5QSWR67T4VYKJXHU3QQGJADA5CNFSM4JB4IC32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECE3TJI#issuecomment-545896869, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIIR2K2MWJMBLFPPKOWTVDTQQGJADANCNFSM4JB4IC3Q .

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