more instruction about how to run fagin?

[hsinyenwu]

Dear Zebulun, I am trying to learn how to use fagin with the yeast dataset. However, after download the data, running make run-yeast resulted in error message. Is there a vignette for running the package available for fagin? Thanks! Best, Larry

[arendsee]

Beyond the case studies, there is not an additional vignette.

If you post the error message, I may be able to help. However, I don't actively maintain this package anymore (I graduated two years ago), so there isn't too much I can do.

[evewurtele]

Hi Larry,

Another student, Jing Li, has done this analysis for yeast data. The preprint is here https://www.biorxiv.org/content/10.1101/671263v2, and you can contact Jing directly (please copy to me, mash@iastate.edu, as well).

Which yeast spp are you interested in?

Best, Eve

On Mon, Dec 21, 2020 at 12:59 PM Zebulun Arendsee notifications@github.com wrote:

Beyond the case studies, there is not an additional vignette.

If you post the error message, I may be able to help. However, I don't actively maintain this package anymore (I graduated two years ago), so there isn't too much I can do.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/arendsee/fagin/issues/23#issuecomment-749138890, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE3D2X7ZU25EGYRR3CWZGQ3SV6LKJANCNFSM4VERKHXQ .

-- Eve Syrkin Wurtele, Professor 515-708-3232 (cell) 441 Bessey Hall, Iowa State Univ. homepage https://www.gdcb.iastate.edu/people/eve-syrkin-wurtele MetNetSoftware and PMR http://metnetweb.gdcb.iastate.edu/ Publications https://scholar.google.com/citations?user=8dM4Cj0AAAAJ&hl=en Meta!Blast computer game https://www.metablastcell.com/

[hsinyenwu]

Dear Eve and Zebulun,

Thanks a lot for your prompt reply. I will follow up with Jing and copy Eve.

I am interested in Arabidopsis but want to try out Fagin with the yeast dataset. Our lab uses ribosome profiling to identify small ORFs on annotated non-coding RNAs in Arabidopsis. We also identified a group of genes that appear to be dual-coding from our latest dataset. We hope to use Fagin to test if these sORFs or overprinted genes are de novo genes. I also copy Polly Hsu in this email.

Best, Larry

On Dec 21, 2020, at 2:10 PM, evewurtele notifications@github.com<mailto:notifications@github.com> wrote:

Hi Larry,

Another student, Jing Li, has done this analysis for yeast data. The preprint is here https://www.biorxiv.org/content/10.1101/671263v2, and you can contact Jing directly (please copy to me, mash@iastate.edumailto:mash@iastate.edu, as well).

Which yeast spp are you interested in?

Best, Eve

On Mon, Dec 21, 2020 at 12:59 PM Zebulun Arendsee notifications@github.com<mailto:notifications@github.com> wrote:

Beyond the case studies, there is not an additional vignette.

If you post the error message, I may be able to help. However, I don't actively maintain this package anymore (I graduated two years ago), so there isn't too much I can do.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/arendsee/fagin/issues/23#issuecomment-749138890, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE3D2X7ZU25EGYRR3CWZGQ3SV6LKJANCNFSM4VERKHXQ .

-- Eve Syrkin Wurtele, Professor 515-708-3232 (cell) 441 Bessey Hall, Iowa State Univ. homepage https://www.gdcb.iastate.edu/people/eve-syrkin-wurtele MetNetSoftware and PMR http://metnetweb.gdcb.iastate.edu/ Publications https://scholar.google.com/citations?user=8dM4Cj0AAAAJ&hl=en Meta!Blast computer game https://www.metablastcell.com/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/arendsee/fagin/issues/23#issuecomment-749145997, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABBOHMNBIEII62HZFBUTIQ3SV6MTJANCNFSM4VERKHXQ.