search

FunctionLab / ExPecto

predicting expression effects of human genome variants ab initio from sequence
116 stars 41 forks source link

About the download of 2002 feature files #19

Open Licko0909 opened 4 years ago

Licko0909 commented 4 years ago

Hi,

I want to get 2002 narrow-peak files of matin features, but I did not provide the link in the file "deepsea_beluga_2002_features.tsv".

I can only download 874 of them through Google search,

I really hope to get a reply,

hank you very much!

Licko0909 commented 4 years ago

874 file from here: https://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/narrowPeak/

jzthree commented 4 years ago

You can get the files from ENCODE project here http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/ http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/

On Thu, Feb 20, 2020 at 5:27 AM Licko0909 notifications@github.com wrote:

874 file from here:

https://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/narrowPeak/

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/FunctionLab/ExPecto/issues/19?email_source=notifications&email_token=AB7SOYZ54TAQXK2S3OZ4ADDRD2OPRA5CNFSM4KYRCMF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMOU37A#issuecomment-589123068, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7SOY4JADCPEEE622WJWVTRD2OPRANCNFSM4KYRCMFQ .

Licko0909 commented 4 years ago

Thank you very much, thank you for your reply!

But， I already have 919 of deepsea's features, and the two links above are for blind deepsea's DHS and TF, a total of 814 narrow-peak files.

My main confusion at the moment is that I can't find the other 1083 features used by expecto, except for Deepsea's 919 narrow-peak files (2002-919=1083). I really hope to get a reply again!

黄立超

13536522254@163.com | 签名由网易邮箱大师定制 On 2/21/2020 03:36，Jian Zhounotifications@github.com wrote： You can get the files from ENCODE project here http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/ http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/

On Thu, Feb 20, 2020 at 5:27 AM Licko0909 notifications@github.com wrote:

874 file from here:

https://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/narrowPeak/

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/FunctionLab/ExPecto/issues/19?email_source=notifications&email_token=AB7SOYZ54TAQXK2S3OZ4ADDRD2OPRA5CNFSM4KYRCMF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMOU37A#issuecomment-589123068, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7SOY4JADCPEEE622WJWVTRD2OPRANCNFSM4KYRCMFQ .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

jzthree commented 4 years ago

The full list of URL is also available here (https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-019-0420-0/MediaObjects/41588_2019_420_MOESM9_ESM.xlsx). Even though some of the URLs are no longer valid as of now even though you should be able to find counterparts on roadmap epigenomics website.

Licko0909 commented 4 years ago

Wow! That great! Thank you very much, thank you for your reply! ^_^!!!!

黄立超

13536522254@163.com | 签名由网易邮箱大师定制 On 2/21/2020 21:10，黄立超13536522254@163.com wrote： Thank you very much, thank you for your reply!

But， I already have 919 of deepsea's features, and the two links above are for blind deepsea's DHS and TF, a total of 814 narrow-peak files.

My main confusion at the moment is that I can't find the other 1083 features used by expecto, except for Deepsea's 919 narrow-peak files (2002-919=1083). I really hope to get a reply again!

黄立超

13536522254@163.com | 签名由网易邮箱大师定制 On 2/21/2020 03:36，Jian Zhounotifications@github.com wrote： You can get the files from ENCODE project here http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/ http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/

On Thu, Feb 20, 2020 at 5:27 AM Licko0909 notifications@github.com wrote:

874 file from here:

https://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/narrowPeak/

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/FunctionLab/ExPecto/issues/19?email_source=notifications&email_token=AB7SOYZ54TAQXK2S3OZ4ADDRD2OPRA5CNFSM4KYRCMF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMOU37A#issuecomment-589123068, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7SOY4JADCPEEE622WJWVTRD2OPRANCNFSM4KYRCMFQ .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

Licko0909 commented 4 years ago

I have found this supplementary data, but the link is invalid;I tried to download this data by other means last week, but I could not verify the correctness

黄立超

13536522254@163.com | 签名由网易邮箱大师定制 On 2/24/2020 08:23，Jian Zhounotifications@github.com wrote：

The full list of URL is also available here (https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-019-0420-0/MediaObjects/41588_2019_420_MOESM9_ESM.xlsx). Even though some of the URLs are no longer valid as of now even though you should be able to find counterparts on roadmap epigenomics website.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.