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larssnip / micropan

R package for microbial pangenomics
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raw data #11

Open jhcuarta opened 2 years ago

jhcuarta commented 2 years ago

Hi I've been having trouble running the script using 442 raw .fna files downloaded from NCBI and extracted to working directory /home/jason/Documents/micropan/fna I had issues trying to construct the genome table, since the recommended video is no longer aviable, and this is used for downloading and downstream command line. I also had inconvinients running mutate function since I can't define Sequence variable as defined in the example. Sorry to bother since I got not much expertise using R.

larssnip commented 2 years ago

Hi,

Would it be best if you emailed me an overview of the 442 genomes, and where they can be downloaded from? Then I may help you get this on track but making the required R code…

LS

From: jhcuarta @.> Sent: lørdag 9. april 2022 06:36 To: larssnip/micropan @.> Cc: Subscribed @.***> Subject: [larssnip/micropan] raw data (Issue #11)

Hi I've been having trouble running the script using 442 raw .fna files downloaded from NCBI and extracted to working directory /home/jason/Documents/micropan/fna I had issues trying to construct the genome table, since the recommended video is no longer aviable, and this is used for downloading and downstream command line. I also had inconvinients running mutate function since I can't define Sequence variable as defined in the example. Sorry to bother since I got not much expertise using R.

— Reply to this email directly, view it on GitHubhttps://github.com/larssnip/micropan/issues/11, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFTGDFI642HHIYKAV7LVEECK5ANCNFSM5S6JXNRA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

jhcuarta commented 2 years ago

Hi All the genomes belong to Vibrio cholerae, I downloaded from NCBI AND renamed them for downstream prefix handling

Regards

El lun., 11 de abril de 2022 2:20 a. m., Lars Snipen < @.***> escribió:

Hi,

Would it be best if you emailed me an overview of the 442 genomes, and where they can be downloaded from? Then I may help you get this on track but making the required R code…

LS

From: jhcuarta @.> Sent: lørdag 9. april 2022 06:36 To: larssnip/micropan @.> Cc: Subscribed @.***> Subject: [larssnip/micropan] raw data (Issue #11)

Hi I've been having trouble running the script using 442 raw .fna files downloaded from NCBI and extracted to working directory /home/jason/Documents/micropan/fna I had issues trying to construct the genome table, since the recommended video is no longer aviable, and this is used for downloading and downstream command line. I also had inconvinients running mutate function since I can't define Sequence variable as defined in the example. Sorry to bother since I got not much expertise using R.

— Reply to this email directly, view it on GitHub< https://github.com/larssnip/micropan/issues/11>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ADJZZFTGDFI642HHIYKAV7LVEECK5ANCNFSM5S6JXNRA>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/larssnip/micropan/issues/11#issuecomment-1094641739, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUY7JFFNNCZCVHQWDFJ3WMTVEPHCDANCNFSM5S6JXNRA . You are receiving this because you authored the thread.Message ID: @.***>

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larssnip commented 2 years ago

Hi again,

First: I have updated the GitHub site for micropan, and the tutorial. There should be a video there now.

For me to help you on this I will need:

  1. A file, e.g. an Excel spreadsheet or something similar, listing the genomes. Their names and the name of the fasta file with the genome for each genome.
  2. A folder with the genome fasta file. This must be compressed into an archive. It may be too big to send by email. Perhaps you could make a smaller subset of the 442 genomes, just to get the code working. I suggest this, select 10 of the genomes, and let us see if we can this on track.

LS

From: jhcuarta @.> Sent: mandag 11. april 2022 09:36 To: larssnip/micropan @.> Cc: Lars-Gustav Snipen @.>; Comment @.> Subject: Re: [larssnip/micropan] raw data (Issue #11)

Hi All the genomes belong to Vibrio cholerae, I downloaded from NCBI AND renamed them for downstream prefix handling

Regards

El lun., 11 de abril de 2022 2:20 a. m., Lars Snipen < @.***> escribió:

Hi,

Would it be best if you emailed me an overview of the 442 genomes, and where they can be downloaded from? Then I may help you get this on track but making the required R code…

LS

From: jhcuarta @.> Sent: lørdag 9. april 2022 06:36 To: larssnip/micropan @.> Cc: Subscribed @.***> Subject: [larssnip/micropan] raw data (Issue #11)

Hi I've been having trouble running the script using 442 raw .fna files downloaded from NCBI and extracted to working directory /home/jason/Documents/micropan/fna I had issues trying to construct the genome table, since the recommended video is no longer aviable, and this is used for downloading and downstream command line. I also had inconvinients running mutate function since I can't define Sequence variable as defined in the example. Sorry to bother since I got not much expertise using R.

— Reply to this email directly, view it on GitHub< https://github.com/larssnip/micropan/issues/11>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ADJZZFTGDFI642HHIYKAV7LVEECK5ANCNFSM5S6JXNRA>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/larssnip/micropan/issues/11#issuecomment-1094641739, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUY7JFFNNCZCVHQWDFJ3WMTVEPHCDANCNFSM5S6JXNRA . You are receiving this because you authored the thread.Message ID: @.***>

-- Aviso legal: El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co http://www.unal.edu.co/. Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

— Reply to this email directly, view it on GitHubhttps://github.com/larssnip/micropan/issues/11#issuecomment-1094654803, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFX4IHLFGY2ANKUK4TDVEPI7HANCNFSM5S6JXNRA. You are receiving this because you commented.Message ID: @.***>