ChatGPT 4o incorrectly suggested to me that it could handle large FASTQ files and run a full analysis pipeline. I am trying to analyze a FASTQ that shows an E coli infection for evidence in the functional genomics that this is acid-adapted strains of E coli known as AIEC. ChatGPT 4o knows the full pipeline of commands to use but when I uploaded the large FASTQ files it gives up and says the files are too large for its processing environment. The two FASTQ files were each under 600 MB.
Is there any Chat LLM currently in existence that can handle larger FASTQ files and do a full analysis against them?
This is almost certainly asking too much of tools like chat GPT. I would encourage you to read through some of the documentation to see if your desired analysis goals are accomplishable with QIIME2 software--but be aware that it will take significant effort on your part.
Take a look at the pipeline that ChatGPT 4o proposed. Not too shabby!
In an analogous way to how these tools are writing brilliant software code, they are also extraordinary at figuring out system administration tasks and building sequences of commands to achieve results.
In an environment that did not have the size restrictions, it would have been useful just to see the pipeline execute, and become familiar with the typical command line inputs and the kinds of outputs you receive. As just a training tool, it would be extraordinary.
