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MD-Anderson-Bioinformatics / SpliceSeq

A tool for investigating alternative mRNA splicing in next generation mRNA sequence data.
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Splice Seq DB connection error #4

Closed k1muk closed 4 years ago

k1muk commented 4 years ago

Hello @mryaninsilico

I am trying to launch a local SpliceSeq.jar file. When I double click it, it throws a connection error while trying to connect to SpliceGraph20 @"jdbc:ratway://projects.insilico.us.com/Ratway/RW".

I would like to work with your sample DB, that has processed data from TCGA. I don't have my own data to create a local DB. I tried using your online version- but it doesn't give me options for comparative analysis or p-values.....

Any work around or pointers on how I can go about resolving this issue, will be much appreciated.

And thank you for this tool!

Thanks, Kavitha

mryaninsilico commented 4 years ago

Kavitha,

Thanks for your interest in SpliceSeq. The easiest way to get TCGA splicing in formation is to use the TCGA SpliceSeq site here: https://bioinformatics.mdanderson.org/TCGASpliceSeq/ or on our beta site that has some new features like clinical data: http://projects.insilico.us.com/TCGASpliceSeq/. You can interactively look at specific genes or go to the download page and get PSI values for each sample / splice event.

Try that out and let me know if you have specific follow up questions.

Thanks,

Mike Ryan, PhD

In Silico Solutions

From: k1muk [mailto:notifications@github.com] Sent: Thursday, January 23, 2020 2:19 PM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Michael Ryan; Mention Subject: [MD-Anderson-Bioinformatics/SpliceSeq] Splice Seq DB connection error (#4)

Hello @mryaninsilico https://github.com/mryaninsilico

I am trying to launch a local SpliceSeq.jar file. When I double click it, it throws a connection error while trying to connect to "jdbc:ratway://projects.insilico.us.com/Ratway/RW" and SpliceGraph

I would like to work with your sample DB, that has processed data from TCGA. I don't have my own data to create a local DB. Any work around or pointers on how I can go about resolving this issue, will be much appreciated.

And thank you for this tool!

Thanks, Kavitha

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MD-Anderson-Bioinformatics/SpliceSeq/issues/4?email_source=notifications&email_token=ADC6Q6ZX2666QJW7F5K4FUTQ7HUSPA5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIKYMMQ , or unsubscribe https://github.com/notifications/unsubscribe-auth/ADC6Q64VFW2DCTPBNZDTFRTQ7HUSPANCNFSM4KK3TXCA . https://github.com/notifications/beacon/ADC6Q6ZZ2Y533NT27SCDXV3Q7HUSPA5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIKYMMQ.gif

k1muk commented 4 years ago

Hello,

Thanks for getting back to me. But, TCGAspliceseq doesn't give me an option to download PSI values for non-tumor samples. Because, when I input sample ids as, say "TCGA-A6-5655", I don't provide the sample type information (01 or 11). Am I missing something here?

My end goal was to identify dPSI for a select set of samples with a TCGA cohort...

Thanks, Kavitha

On Thu, Jan 23, 2020 at 11:30 AM Michael Ryan notifications@github.com wrote:

Kavitha,

Thanks for your interest in SpliceSeq. The easiest way to get TCGA splicing in formation is to use the TCGA SpliceSeq site here: https://bioinformatics.mdanderson.org/TCGASpliceSeq/ or on our beta site that has some new features like clinical data: http://projects.insilico.us.com/TCGASpliceSeq/. You can interactively look at specific genes or go to the download page and get PSI values for each sample / splice event.

Try that out and let me know if you have specific follow up questions.

Thanks,

Mike Ryan, PhD

In Silico Solutions

From: k1muk [mailto:notifications@github.com] Sent: Thursday, January 23, 2020 2:19 PM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Michael Ryan; Mention Subject: [MD-Anderson-Bioinformatics/SpliceSeq] Splice Seq DB connection error (#4)

Hello @mryaninsilico https://github.com/mryaninsilico

I am trying to launch a local SpliceSeq.jar file. When I double click it, it throws a connection error while trying to connect to "jdbc:ratway:// projects.insilico.us.com/Ratway/RW" and SpliceGraph

I would like to work with your sample DB, that has processed data from TCGA. I don't have my own data to create a local DB. Any work around or pointers on how I can go about resolving this issue, will be much appreciated.

And thank you for this tool!

Thanks, Kavitha

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/MD-Anderson-Bioinformatics/SpliceSeq/issues/4?email_source=notifications&email_token=ADC6Q6ZX2666QJW7F5K4FUTQ7HUSPA5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIKYMMQ> , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADC6Q64VFW2DCTPBNZDTFRTQ7HUSPANCNFSM4KK3TXCA> . < https://github.com/notifications/beacon/ADC6Q6ZZ2Y533NT27SCDXV3Q7HUSPA5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIKYMMQ.gif>

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MD-Anderson-Bioinformatics/SpliceSeq/issues/4?email_source=notifications&email_token=AM3BSW5HE7XTPEZLRDQ34T3Q7HV43A5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJYRWPA#issuecomment-577837884, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM3BSW6LRGCJZXRHF577HJ3Q7HV43ANCNFSM4KK3TXCA .

mryaninsilico commented 4 years ago

Kavitha,

When you download PSI values, you can leave the sample id specification empty and it will download all samples for the tumor type selected. The sample IDs that end with ‘_Norm’ are the matched normal samples. For samples that have adjacent normal sequencing, you will get two columns in the download PSI matrix, one like TCGA-A6-5655 for the tumor sample and the other like TCGA-A6-5655_Norm.

Mike

From: k1muk [mailto:notifications@github.com] Sent: Monday, January 27, 2020 1:10 PM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Michael Ryan; Mention Subject: Re: [MD-Anderson-Bioinformatics/SpliceSeq] Splice Seq DB connection error (#4)

Hello,

Thanks for getting back to me. But, TCGAspliceseq doesn't give me an option to download PSI values for non-tumor samples. Because, when I input sample ids as, say "TCGA-A6-5655", I don't provide the sample type information (01 or 11). Am I missing something here?

My end goal was to identify dPSI for a select set of samples with a TCGA cohort...

Thanks, Kavitha

On Thu, Jan 23, 2020 at 11:30 AM Michael Ryan notifications@github.com wrote:

Kavitha,

Thanks for your interest in SpliceSeq. The easiest way to get TCGA splicing in formation is to use the TCGA SpliceSeq site here: https://bioinformatics.mdanderson.org/TCGASpliceSeq/ or on our beta site that has some new features like clinical data: http://projects.insilico.us.com/TCGASpliceSeq/. You can interactively look at specific genes or go to the download page and get PSI values for each sample / splice event.

Try that out and let me know if you have specific follow up questions.

Thanks,

Mike Ryan, PhD

In Silico Solutions

From: k1muk [mailto:notifications@github.com] Sent: Thursday, January 23, 2020 2:19 PM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Michael Ryan; Mention Subject: [MD-Anderson-Bioinformatics/SpliceSeq] Splice Seq DB connection error (#4)

Hello @mryaninsilico https://github.com/mryaninsilico

I am trying to launch a local SpliceSeq.jar file. When I double click it, it throws a connection error while trying to connect to "jdbc:ratway:// projects.insilico.us.com/Ratway/RW" and SpliceGraph

I would like to work with your sample DB, that has processed data from TCGA. I don't have my own data to create a local DB. Any work around or pointers on how I can go about resolving this issue, will be much appreciated.

And thank you for this tool!

Thanks, Kavitha

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/MD-Anderson-Bioinformatics/SpliceSeq/issues/4?email_source=notifications https://github.com/MD-Anderson-Bioinformatics/SpliceSeq/issues/4?email_source=notifications&email_token=ADC6Q6ZX2666QJW7F5K4FUTQ7HUSPA5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIKYMMQ &email_token=ADC6Q6ZX2666QJW7F5K4FUTQ7HUSPA5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIKYMMQ> , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADC6Q64VFW2DCTPBNZDTFRTQ7HUSPANCNFSM4KK3TXCA> . < https://github.com/notifications/beacon/ADC6Q6ZZ2Y533NT27SCDXV3Q7HUSPA5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIKYMMQ.gif>

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/MD-Anderson-Bioinformatics/SpliceSeq/issues/4?email_source=notifications https://github.com/MD-Anderson-Bioinformatics/SpliceSeq/issues/4?email_source=notifications&email_token=AM3BSW5HE7XTPEZLRDQ34T3Q7HV43A5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJYRWPA#issuecomment-577837884 &email_token=AM3BSW5HE7XTPEZLRDQ34T3Q7HV43A5CNFSM4KK3TXCKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJYRWPA#issuecomment-577837884>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM3BSW6LRGCJZXRHF577HJ3Q7HV43ANCNFSM4KK3TXCA .

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k1muk commented 4 years ago

Hello, So sorry, my bad, I never noticed the "_norm" column names. I had downloaded the entire file much earlier. I guess, I should have just parsed it, rather than giving it a visual inspection :) Thanks again! -Kavitha