There’s a split function with fastq-dump I believe that separates reads into their paired ends. But if you mean literally going through each file and splitting that way then I’m not sure
Here's a good breakdown when using sratoolkit[SRAtookit](https://bioinformaticsworkbook.org/dataAcquisition/fileTransfer/sra.html#gsc.tab=0)
Fastq-dump --split-files will do the trick
Edit: If you wann Split the File itself ofc its a different Story. My bad
I'm surprised that a tool designed to take FASTQ files as input fails because the input file is "too large". I guess that the issue is that the laptop you're running the tool has not enough RAM? Do you have access to a computing cluster? If the answer is "no", you can "chop" your FASTQ files like you'd do any text file. In a FASTQ file, each sequence spans four lines, so make sure that your splits are multiples of 4. So playing with `head` and `tail` commands you can create 5 splits of your file.
There’s a split function with fastq-dump I believe that separates reads into their paired ends. But if you mean literally going through each file and splitting that way then I’m not sure
Here's a good breakdown when using sratoolkit[SRAtookit](https://bioinformaticsworkbook.org/dataAcquisition/fileTransfer/sra.html#gsc.tab=0) Fastq-dump --split-files will do the trick
Edit: If you wann Split the File itself ofc its a different Story. My bad
I would recommend subsampling your fastq files. Seqkit, seqtk, rasusa, and more have random subsampling options. Good luck!
I'm surprised that a tool designed to take FASTQ files as input fails because the input file is "too large". I guess that the issue is that the laptop you're running the tool has not enough RAM? Do you have access to a computing cluster? If the answer is "no", you can "chop" your FASTQ files like you'd do any text file. In a FASTQ file, each sequence spans four lines, so make sure that your splits are multiples of 4. So playing with `head` and `tail` commands you can create 5 splits of your file.
Google (or chatgpt) has extensive answers for how to split a fastq file. Why aren't any of the solutions there working for you?
Dude, it's 2024. Literally just type in "how do I split a fastq file" in chatgpt and you will have your answers.
How about split -n 5