Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 6 2023 Mar 20, Spring 7 2023 Apr 10
Description
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3.
We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue.
To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not.
Previously, we have found that the plant selective marker gene was expressed in soybean seeds in a transgenic line.
For this task, we'll investigate whether we can use the F3H-OX3 line's plant selection marker gene to distinguish transgenic from non-transgenic lines.
See:
- Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z
- Code repository: https://bitbucket.org/lorainelab/soyseq
Maarten has sent us three files with the construct information in them. These are added to the git repository here:
- ExternalDataSets/pK7WG2-F3H.fa
- ExternalDataSets/pK7WG2-F3H.gb
In this experiment, the plant selection gene was a kanamycin resistance gene.
For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene.
To do this, we need to investigate the different tools that might be available for this task.
Let's try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence.
Attachments
Issue Links
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
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| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Molly Davis [ molly ] |
| Summary | Distinguish F3H-OX3 from VF36 samples | Investigate: Distinguish F3H-OX3 from VF36 samples |
| Description |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. We will add these to repository in the ExternalDataSets folder, after removing the whitespace in the file names. For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin gene. To do this, we need to investigate the different tools that might be available for this task. First, let's devote some time to searching for an easy-to-use effective tool that will be able to identify which samples contain "kan" gene sequences. |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. We will add these to repository in the ExternalDataSets folder, after removing the whitespace in the file names. For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin gene. To do this, we need to investigate the different tools that might be available for this task. Try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. We will add these to repository in the ExternalDataSets folder, after removing the whitespace in the file names. For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin gene. To do this, we need to investigate the different tools that might be available for this task. Try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. We will add these to repository in the ExternalDataSets folder, after removing the whitespace in the file names. For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene. To do this, we need to investigate the different tools that might be available for this task. Try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
| Sprint | Spring 6 2023 Mar 20 [ 166 ] | Spring 6 2023 Mar 20, Spring 7 2023 Apr 10 [ 166, 167 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Description |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. We will add these to repository in the ExternalDataSets folder, after removing the whitespace in the file names. For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene. To do this, we need to investigate the different tools that might be available for this task. Try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. These are added to the git repository: For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene. To do this, we need to investigate the different tools that might be available for this task. Try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
| Description |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. These are added to the git repository: For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene. To do this, we need to investigate the different tools that might be available for this task. Try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. These are added to the git repository here: * ExternalDataSets/pK7WG2-F3H.fa * ExternalDataSets/pK7WG2-F3H.gb For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene. To do this, we need to investigate the different tools that might be available for this task. Try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
| Link | This issue relates to IGBF-3306 [ IGBF-3306 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Assignee | Molly Davis [ molly ] | Robert Reid [ robertreid ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Description |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the kanamycin selection gene was expressed in soybean seeds in a transgenic line. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. These are added to the git repository here: * ExternalDataSets/pK7WG2-F3H.fa * ExternalDataSets/pK7WG2-F3H.gb For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene. To do this, we need to investigate the different tools that might be available for this task. Try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
Muday Lab has detected possible sample switching in their time course data from three genotypes: ARE (mutant), F3H-OX3 (transgenic), and VF36 (wild-type, parent strain for F3H-OX3)
It was easy to identify which samples were ARE and not VF36 or F3H-OX3. We need a way to distinguish F3H-OX3 from VF36 samples due to the sample switching issue. To do this, we can use the fact that F3H-OX3 contains transgenic construct and VF36 does not. Previously, we have found that the plant selective marker gene was expressed in soybean seeds in a transgenic line. For this task, we'll investigate whether we can use the F3H-OX3 line's plant selection marker gene to distinguish transgenic from non-transgenic lines. See: * Open access article link: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-015-0207-z * Code repository: https://bitbucket.org/lorainelab/soyseq Maarten has sent us three files with the construct information in them. These are added to the git repository here: * ExternalDataSets/pK7WG2-F3H.fa * ExternalDataSets/pK7WG2-F3H.gb In this experiment, the plant selection gene was a kanamycin resistance gene. For this task, use the kanamycin gene either as a query or a target in a search of the fastq files to identify samples that contain RNA-Seq reads from the kanamycin-resistance gene. To do this, we need to investigate the different tools that might be available for this task. Let's try to find an easy-to-use tool or approach that will let us identify RNA-Seq samples containing "kan" gene sequence. |
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| Assignee | Molly Davis [ molly ] | Robert Reid [ robertreid ] |