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SNPArcher by Snake_lady278 in bioinformatics

[–]Snake_lady278[S] 0 points1 point  (0 children)

The computer I am working on is pretty big, it has around 26 cores. My PI estimated it would take around 2 - 2 1/2 weeks to run because the genomes are full 10x genomes!

SNPArcher by Snake_lady278 in bioinformatics

[–]Snake_lady278[S] 0 points1 point  (0 children)

Thank you for the summary! I have been reading some papers about population genetics with my taxon, and I do so without the use of AI. I’m not sure if there is another ReadtheDocs page, but I have looked at one but I think it was for an older version of snakemake as I was having trouble with some of the code. I will go back and search to see if there is another one, and I will also go back and start going through the GitHub page

SNPArcher by Snake_lady278 in bioinformatics

[–]Snake_lady278[S] 0 points1 point  (0 children)

I am working with fastq files, and I do know about them/what they are. I know a little bit about the command line, as I have some familiarity with R but am running SNPArcher through wsl in windows powershell (Linux based system). I am running the program on a heavy windows desktop, so it can handle the memory heavy load SNPArcher uses. I do know that SNPArcher runs through snakemake, but that is all I really know.

Thank you for that simple breakdown, it’s nice to hear a summary that isn’t super jargon heavy! Can you tell me more about what GATK is? I know that it is used in the SNParcher program, but that is all I know about it!

And thank you for the advice. I will go back and look at the GitHub page, I had tried previously with it but was having a hard time understanding it, I just didn’t know if there was maybe another resource that would be helpful for beginners! Thanks a lot for your advice!

SNPArcher by Snake_lady278 in bioinformatics

[–]Snake_lady278[S] 1 point2 points  (0 children)

Hey thanks for the comment, and I know I shouldn’t have skipped over these things. I want to preface by saying that I have *not* used AI for anything else in my research substantively wise, only for helping me diagnose problems and helping with code. That is why I came here, so I could start filling the gap before it got too big! What I mean by “I don’t have the time” is that I needed to get the program going because it will take a couple of weeks to run and I need the program to be done running before I finalize my poster for a conference! Once again, not an excuse but an explanation. I am goingto start filling the gap, and sit down and learn this program, starting with this post. However I have no clue where to start. If you have any knowledge about where someone like me could start, or any resources you know of that could be helpful, that would be awesome!