Can I simply rename a Illumina sequencing file (fastq format) that is named as .txt to .fastq without having any problems?

Question

[Beginner]

Hi,

I am relatively new to the analysis of sequencing data. I got some sequencing data as a .txt file that seems to have the normal fastq format. Since fastq is a txt file, can I simply rename the files from "myData.txt" to "myData.fastq" or from "myData.txt.gz" to "myData.fastq.gz" without having any issues? Is making it a .fastq file even necessary for downstream analysis or will inputting it as a .txt file e.g. for FastQC or mapping with STAR give exactly the same result? Also, I know that most programs accept fastq.gz files. If .txt and .fastq is kind of the same file format, can I also use .txt.gz as an input for those programs, since unpacking all those files gets a little heavy on my disk space.

Thanks for your help!

[Beginner]

Thank you, your answers helped!

Answer 1

[GenoMax]

If you are sure you have a valid fastq file then you can safely re-name it from .txt to .fastq. If a file is gzip-compressed then you can't use it as an input to a program that expects plain fastq files. That said most next generation sequencing programs should handle gzip compressed files (Disclaimer: some may need specific program options e.g. STAR, YMMV depending on program you are using).

Answer 2

[Kevin Blighe]

I would stick to the convention and name them based on how the data is arranged inside the files. FASTQ is just a file extension but also describes a layout... a way to arrange sequence data. The data is indeed just plain text, but I would say that the file extension is important, even if programs can tolerate any extension.

If you can confirm that the data is in FASTQ format, then you should name them FASTQ.

Kevin