basespace-developers

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Thank you for visiting the BaseSpace Sequence Hub developers Google group. This group is not active, and we are no longer monitoring this page. We encourage you to visit our software resources page at https://developer.illumina.com. For further assistance, please contact our Technical Support team: techsupport@illumina.com.

We appreciate your many contributions throughout the years!

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Christian Jansen, Al Maynard5

1/13/23

App startup loop

Hi Christian, Unfortunately, your timing isn't great... This group has been shut down - please

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App startup loop

Hi Christian, Unfortunately, your timing isn't great... This group has been shut down - please

1/13/23

12/26/22

API Versions and Long-Term Support

Hi there, Are the V2 APIs designed to replace V1 or complement them? Are there plans to discontinue

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API Versions and Long-Term Support

Hi there, Are the V2 APIs designed to replace V1 or complement them? Are there plans to discontinue

12/26/22

12/22/22

Basespace API keys

Hi Team, Do we have any docs on API keys for construction of app launches via POST. eg POST body {

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Basespace API keys

Hi Team, Do we have any docs on API keys for construction of app launches via POST. eg POST body {

12/22/22

Christian Jansen3

12/1/22

Report stuck at rendering

Dear community, one more update form my side. After starting to adjust the report of my app to show

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Report stuck at rendering

Dear community, one more update form my side. After starting to adjust the report of my app to show

12/1/22

Alexandre Moura

10/24/22

Cufflinks issue?

Hi there, After launching Cufflinks from an ongoing project, I wasn't able to select the datasets

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Cufflinks issue?

Hi there, After launching Cufflinks from an ongoing project, I wasn't able to select the datasets

10/24/22

Alexandre Moura, Nick Vinckier3

10/20/22

Header information error

Thank you, Nick! On Tuesday, October 18, 2022 at 10:00:49 AM UTC-4 Nick Vinckier wrote: It looks like

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Header information error

Thank you, Nick! On Tuesday, October 18, 2022 at 10:00:49 AM UTC-4 Nick Vinckier wrote: It looks like

10/20/22

Christian Jansen, Nick Vinckier6

10/19/22

Request could not be processed

Hi everyone, For future reference I managed to fix the issue on my own. It seems to have been linked

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Request could not be processed

Hi everyone, For future reference I managed to fix the issue on my own. It seems to have been linked

10/19/22

Patricia Oliveira

10/14/22

Diferences between gvcf and vcf hard filtered variants

Hi! With the new 4.0 DRAGEN Enrichment version, they now provide us with 2 hard.filtered json files:

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Diferences between gvcf and vcf hard filtered variants

Hi! With the new 4.0 DRAGEN Enrichment version, they now provide us with 2 hard.filtered json files:

10/14/22

Mariko T, … Patricia Oliveira4

10/14/22

Download AppResults files at once

Hi! Can you also download only specific files from an analysis within a project? Cheers Pat On

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Download AppResults files at once

Hi! Can you also download only specific files from an analysis within a project? Cheers Pat On

10/14/22

9/30/22

Can a Native App Create New Samples?

Is a Native App able to create a new sample by uploading Fastqs to /data/output/samples/<project-

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Can a Native App Create New Samples?

Is a Native App able to create a new sample by uploading Fastqs to /data/output/samples/<project-

9/30/22

9/16/22

Hi Team, I have recently started having issues with the https://api.basespace.illumina.com/v1pre3/

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Hi Team, I have recently started having issues with the https://api.basespace.illumina.com/v1pre3/

9/16/22

9/7/22

Basespace Native App Development

Dear Team, I am trying to follow the steps as given in https://developer.basespace.illumina.com/docs/

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Basespace Native App Development

Dear Team, I am trying to follow the steps as given in https://developer.basespace.illumina.com/docs/

9/7/22

9/6/22

Re: [basespace-developers] time out error message

Hi, Neta, The last info you shared is related to your personal basespace account and access. Are you

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Re: [basespace-developers] time out error message

Hi, Neta, The last info you shared is related to your personal basespace account and access. Are you

9/6/22

Mariko T, Nick Vinckier3

8/22/22

How to select specific runs under the same project ID to download the fastq files

Hi Nick! Thank you for your reply and it's really helpful. Would you mind giving me some advice

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How to select specific runs under the same project ID to download the fastq files

Hi Nick! Thank you for your reply and it's really helpful. Would you mind giving me some advice

8/22/22

Edson Zandamela, kjth...@me.com3

8/18/22

Download Fastq files from Basespace and Upload to AWS S3 Automatically

Ohhh cool, so do you have to download the "new/missing" FASTQ files from Basespace to the

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Download Fastq files from Basespace and Upload to AWS S3 Automatically

Ohhh cool, so do you have to download the "new/missing" FASTQ files from Basespace to the

8/18/22

7/27/22

CLI New Samples Missing after dataset copy

Hello All, I've two issues that I am hoping to get some help for, I am using CLI and below is my

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CLI New Samples Missing after dataset copy

Hello All, I've two issues that I am hoping to get some help for, I am using CLI and below is my

7/27/22

7/26/22

Combine Fastq from multiple runs

Hi I am trying to use CLI to merge Fastq from a single sample. I can do that using web browser by

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Combine Fastq from multiple runs

Hi I am trying to use CLI to merge Fastq from a single sample. I can do that using web browser by

7/26/22

Tobias Meißner, … Sarah10

7/8/22

basemount - user permissions

Hello, I am running into a similar issue as discussed here by JvanEyll in 2016. Has a better way been

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basemount - user permissions

Hello, I am running into a similar issue as discussed here by JvanEyll in 2016. Has a better way been

7/8/22

Ziv Lang, Ben Moore6

6/20/22

BaseSpace CLI issues

I think it's ok now. Thanks. ב-יום שישי, 17 ביוני 2022 בשעה 21:20:51 UTC+3, ‪Ziv Lang‬‏ כתב/ה: Hi

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BaseSpace CLI issues

I think it's ok now. Thanks. ב-יום שישי, 17 ביוני 2022 בשעה 21:20:51 UTC+3, ‪Ziv Lang‬‏ כתב/ה: Hi

6/20/22

Sandro Regis Cardoso

6/2/22

Newbie on the crowd

Hello fellows, I am just starting and please I would like to know the meaning of QC on FastQC sample.

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Newbie on the crowd

Hello fellows, I am just starting and please I would like to know the meaning of QC on FastQC sample.

6/2/22

Quentin Chartreux

4/18/22

Ora compression

Does anyone know if there are plans to add ora compression to Basespace and if so, when.

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Ora compression

Does anyone know if there are plans to add ora compression to Basespace and if so, when.

4/18/22

Quentin Chartreux

4/18/22

De Novo scoring

Hi all, I would like to know if any of you understand the dq score? This page says to use a default

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De Novo scoring

Hi all, I would like to know if any of you understand the dq score? This page says to use a default

4/18/22

Andreu Paytuvi, Al Maynard2

4/17/22

Big data inside Docker image?

I'd recommend not including in the docker image. Instead I'd consider downloading the files

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Big data inside Docker image?

I'd recommend not including in the docker image. Instead I'd consider downloading the files

4/17/22

Andreu Paytuvi, … Al Maynard6

4/6/22

Error with /genomes

Probably best to reach out to tech support with your details. It should be there! On Wed, Apr 6, 2022

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Error with /genomes

Probably best to reach out to tech support with your details. It should be there! On Wed, Apr 6, 2022

4/6/22

Andreu Paytuvi, Al Maynard2

3/30/22

How the validation works?

Hi Andreu, I'd recommend trying to run a standard app on that biosample first (FASTQ Toolkit?).

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How the validation works?

Hi Andreu, I'd recommend trying to run a standard app on that biosample first (FASTQ Toolkit?).

3/30/22

Mette Voldby Larsen

3/29/22

Closing published apps

Hello basespace-developers' community I was adviced by the BaseSpace Technical Support to post my

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Closing published apps

Hello basespace-developers' community I was adviced by the BaseSpace Technical Support to post my

3/29/22

Gordon Beattie2

3/9/22

CLI Upload: FASTQ naming restrictions don't allow dual index reads (10x data)

Sorry, just realised I forgot to mention, this is single-cell ATAC data from the 10x pipeline, hence

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CLI Upload: FASTQ naming restrictions don't allow dual index reads (10x data)

Sorry, just realised I forgot to mention, this is single-cell ATAC data from the 10x pipeline, hence

3/9/22

2/17/22

BCL and FASTQ to S3

We'd like to set up an automated system for saving both the BCL and FASTQ files to S3. I know we

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BCL and FASTQ to S3

We'd like to set up an automated system for saving both the BCL and FASTQ files to S3. I know we

2/17/22

2/15/22

Send invitation automatically

Hi all, Is it possible through BS cli or API to share a project? ie, to automatically send an

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Send invitation automatically

Hi all, Is it possible through BS cli or API to share a project? ie, to automatically send an

2/15/22

Darren Wight, José Ferrão2

2/8/22

sha256sums for fastq.gz files on Basespace Sequence Hub

Hi Darren, We also using our own script to backup data from basespace into our storage, and I have

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sha256sums for fastq.gz files on Basespace Sequence Hub

Hi Darren, We also using our own script to backup data from basespace into our storage, and I have

2/8/22

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