SEA-PHAGES | All posts created by mespariz

Link to this post \| posted yesterday, 14:50
mespariz	lhughes Hi Steve, If you can't get the DNAM workaround from Kristen to work for your class, I'm happy to share how we use PECAAN in our classes (slides and other resources). We use PECAAN first in our annotation classes. Lee Lee, Thank you for sharing these resources. I came across your message from two years ago and found it very relevant to our current situation. If the offer still stands, I would be extremely grateful to receive your PECAAN slides and any additional teaching materials you've used in your classes. We've experienced ongoing challenges with DNAM installations in our cohort, and I'm evaluating whether PECAAN could serve as a comprehensive replacement for our entire workflow. Specifically, I'm wondering if it can handle the complete workflow, including QC submission and "Review to Improve" step. If you've made any updates to your approach since your original post or have insights about potential limitations, I would greatly appreciate your guidance. Thank you for your time and expertise, and please accept my apologies for reviving an older thread. Best regards, Martín

Link to this post | posted yesterday, 14:50

lhughes
Hi Steve,

If you can't get the DNAM workaround from Kristen to work for your class, I'm happy to share how we use PECAAN in our classes (slides and other resources). We use PECAAN first in our annotation classes.

Lee

Lee, Thank you for sharing these resources. I came across your message from two years ago and found it very relevant to our current situation. If the offer still stands, I would be extremely grateful to receive your PECAAN slides and any additional teaching materials you've used in your classes.

We've experienced ongoing challenges with DNAM installations in our cohort, and I'm evaluating whether PECAAN could serve as a comprehensive replacement for our entire workflow. Specifically, I'm wondering if it can handle the complete workflow, including QC submission and "Review to Improve" step.

If you've made any updates to your approach since your original post or have insights about potential limitations, I would greatly appreciate your guidance.

Thank you for your time and expertise, and please accept my apologies for reviving an older thread.

Best regards,

Martín

Posted in: PECAAN → Teaching with PECAAN

Link to this post \| posted 01 Aug, 2023 19:46
mespariz	Hi Kristen, I followed your steps and successfully obtained an updated version of DNA Master. However, I'm facing an issue when trying to open a previously saved dnam5 file. I'm receiving a "Database Failure" message, which is causing all the dnam5 files to appear empty. It seems like there might be a problem with the database. Could you please assist me in resolving this issue? Your help would be greatly appreciated. Thank you, Martín

Link to this post | posted 01 Aug, 2023 19:46

mespariz

Hi Kristen,

I followed your steps and successfully obtained an updated version of DNA Master. However, I'm facing an issue when trying to open a previously saved dnam5 file. I'm receiving a "Database Failure" message, which is causing all the dnam5 files to appear empty. It seems like there might be a problem with the database. Could you please assist me in resolving this issue? Your help would be greatly appreciated.

Thank you,
Martín

Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701

Link to this post \| posted 01 Jun, 2023 02:13
mespariz	debbie Hi Martin, The final file is a correctly formatted .dnam5 file. It is not a "profile". What file are you working with? Here is the final file submission instructions. https://seaphagesbioinformatics.helpdocsonline.com/article-49 Once I know what you are working with i ca help more. debbie Thank you for your prompt response! I'm currently creating the genome profile so that I can obtain the CSV file for the 'Review to Improve' process. I have attached a screenshot for reference. I would greatly appreciate any assistance you can provide. Best regards, Martín 323Kb

Link to this post | posted 01 Jun, 2023 02:13

mespariz

debbie
Hi Martin,
The final file is a correctly formatted .dnam5 file. It is not a "profile".
What file are you working with?
Here is the final file submission instructions.
https://seaphagesbioinformatics.helpdocsonline.com/article-49

Once I know what you are working with i ca help more.
debbie

Thank you for your prompt response! I'm currently creating the genome profile so that I can obtain the CSV file for the 'Review to Improve' process. I have attached a screenshot for reference. I would greatly appreciate any assistance you can provide.

Best regards,
Martín

Posted in: DNA Master → Can´t make profile

Link to this post \| posted 01 Jun, 2023 02:13
mespariz	debbie Hi Martin, The final file is a correctly formatted .dnam5 file. It is not a "profile". What file are you working with? Here is the final file submission instructions. https://seaphagesbioinformatics.helpdocsonline.com/article-49 Once I know what you are working with i ca help more. debbie Thank you for your prompt response! I'm currently creating the genome profile so that I can obtain the CSV file for the 'Review to Improve' process. I have attached a screenshot for reference. I would greatly appreciate any assistance you can provide. Best regards, Martín 323Kb

Link to this post | posted 01 Jun, 2023 02:13

mespariz

debbie
Hi Martin,
The final file is a correctly formatted .dnam5 file. It is not a "profile".
What file are you working with?
Here is the final file submission instructions.
https://seaphagesbioinformatics.helpdocsonline.com/article-49

Once I know what you are working with i ca help more.
debbie

Posted in: DNA Master → Can´t make profile

Link to this post \| posted 01 Jun, 2023 01:31
mespariz	Hi all, I'm ready to submit the files to phagesdb.org. However, when I try to create the profile for the final annotation, I receive the message "'3.0' is not a valid floating point value". I haven't been able to find a solution to this issue. Can anyone provide any assistance? Thank you in advance. Martín UNR

Posted in: DNA Master → Can´t make profile

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