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cougarlj / COMPSRA

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis
https://regepi.bwh.harvard.edu/circurna/
GNU General Public License v3.0
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piRbase_mm10.obj related #46

Open alberttai opened 1 year ago

alberttai commented 1 year ago

Hi,

I've been trying to download the piRBase_mm10.obj from the https://regepi.bwh.harvard.edu/circurna/bundle_v1/prebuilt_db with no success. I was able to download the piR_mm9_v1.0.bed.gz and the mm9TiMm10.over.chain.gz and the software is presumably trying to re-build the piRBase_mm10.obj using this two files, but list many "failed to match" entries. Here are a few examples:

INFO 2022-09-16 16:08:17 LiftOver Interval piR-mmu-42005247 failed to match chain 3 because intersection length 20 < minMatchSize 26.599999999999998 (0.71428573 < 0.95) INFO 2022-09-16 16:08:17 LiftOver Interval piR-mmu-33018667 failed to match chain 3 because intersection length 23 < minMatchSize 29.45 (0.7419355 < 0.95) INFO 2022-09-16 16:08:17 LiftOver Interval piR-mmu-39819957 failed to match chain 3 because intersection length 22 < minMatchSize 27.549999999999997 (0.7586207 < 0.95) INFO 2022-09-16 16:08:17 LiftOver Interval piR-mmu-39819956 failed to match chain 3 because intersection length 22 < minMatchSize 26.599999999999998 (0.78571427 < 0.95)

However, I would really like to use the most recent version of the piRBase (V3.0). I am able to download the "mmu.align.bed.gz" bed file from the piRBase site, and some other. Is there a way that I can build this object myself using the bed and other files from this website? I saw that there is a -Build command in COMPSRA, but not sure how and if it can be used for this purpose.

Thank you.

cougarlj commented 1 year ago

Dear alberttai,

Thank you for using COMPSRA in your study. The pre-built *.obj objects were built through the Toolkits which are integrated in COMPSRA. You can use it to build the new database, but you still couldn't use the new database for annotation, because we fixed some configuration in the source code. We are now building COMPSRA2 and the user-defined database function would be totally opened. Also, the newest piRBase would be set in default.

Best Wishes, Jiang

On Sat, Sep 17, 2022 at 4:13 AM alberttai @.***> wrote:

Hi,

I've been trying to download the piRBase_mm10.obj from the https://regepi.bwh.harvard.edu/circurna/bundle_v1/prebuilt_db with no success. I was able to download the piR_mm9_v1.0.bed.gz and the mm9TiMm10.over.chain.gz and the software is presumably trying to re-build the piRBase_mm10.obj using this two files, but list many "failed to match" entries. Here are a few examples:

INFO 2022-09-16 16:08:17 LiftOver Interval piR-mmu-42005247 failed to match chain 3 because intersection length 20 < minMatchSize 26.599999999999998 (0.71428573 < 0.95) INFO 2022-09-16 16:08:17 LiftOver Interval piR-mmu-33018667 failed to match chain 3 because intersection length 23 < minMatchSize 29.45 (0.7419355 < 0.95) INFO 2022-09-16 16:08:17 LiftOver Interval piR-mmu-39819957 failed to match chain 3 because intersection length 22 < minMatchSize 27.549999999999997 (0.7586207 < 0.95) INFO 2022-09-16 16:08:17 LiftOver Interval piR-mmu-39819956 failed to match chain 3 because intersection length 22 < minMatchSize 26.599999999999998 (0.78571427 < 0.95)

However, I would really like to use the most recent version of the piRBase (V3.0). I am able to download the "mmu.align.bed.gz" bed file from the piRBase site, and some other. Is there a way that I can build this object myself using the bed and other files from this website? I saw that there is a -Build command in COMPSRA, but not sure how and if it can be used for this purpose.

Thank you.

— Reply to this email directly, view it on GitHub https://github.com/cougarlj/COMPSRA/issues/46, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGMAD52LX7UBTTQEVIHWFDV6TIINANCNFSM6AAAAAAQOUIAHI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

beyond-tan commented 1 year ago

Dear Jiang, I had the same problem. WARN edu.harvard.channing.compass.db.DB_piRBase - The prebuilt database file COMPSRA/bundle_v1/prebuilt_db/piRBase_mm10.obj doesn't exist! Could you provide this object, piRBase_mm10.obj? Thank you.

cougarlj commented 1 year ago

Is it possible to download it from https://regepi.bwh.harvard.edu/circurna/bundle_v1/prebuilt_db ? Because the size of mouse piRNAs pre-built database was dramatically larger than human, it's difficult to handle it.

beyond-tan commented 1 year ago

Is it possible to download it from https://regepi.bwh.harvard.edu/circurna/bundle_v1/prebuilt_db ? Because the size of mouse piRNAs pre-built database was dramatically larger than human, it's difficult to handle it.

I can't download it from the link. The error information is 500: Internal Server Error. Counld you provide the other link?

cougarlj commented 1 year ago

Dear Beyond-tan,

I have reported the error to the IT department and they are transferring the resource to a new place (on Google). I will update the resource address immediately when I get the detailed information from our IT department.

Best Wishes, Jiang Li

On Thu, Sep 22, 2022 at 10:25 AM beyond-tan @.***> wrote:

Is it possible to download it from https://regepi.bwh.harvard.edu/circurna/bundle_v1/prebuilt_db ? Because the size of mouse piRNAs pre-built database was dramatically larger than human, it's difficult to handle it.

I can't download it from the link. The error information is 500: Internal Server Error. Counld you provide the other link?

— Reply to this email directly, view it on GitHub https://github.com/cougarlj/COMPSRA/issues/46#issuecomment-1254433263, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGMAD7C7IAEZTMCXQTSSCDV7O7SHANCNFSM6AAAAAAQOUIAHI . You are receiving this because you commented.Message ID: @.***>

beyond-tan commented 1 year ago

Dear Beyond-tan, I have reported the error to the IT department and they are transferring the resource to a new place (on Google). I will update the resource address immediately when I get the detailed information from our IT department. Best Wishes, Jiang Li … On Thu, Sep 22, 2022 at 10:25 AM beyond-tan @.> wrote: Is it possible to download it from https://regepi.bwh.harvard.edu/circurna/bundle_v1/prebuilt_db ? Because the size of mouse piRNAs pre-built database was dramatically larger than human, it's difficult to handle it. I can't download it from the link. The error information is 500: Internal Server Error. Counld you provide the other link? — Reply to this email directly, view it on GitHub <#46 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGMAD7C7IAEZTMCXQTSSCDV7O7SHANCNFSM6AAAAAAQOUIAHI . You are receiving this because you commented.Message ID: @.>

Thanks a lot.