Can a FASTQ file have two FASTQ files?
If a sample has two fastq files it is likely that the reads are paired end. It is to note however that with a single file it is not possible to exclude that paired end reads can be interleaved in one single file, even if it is not common (in my opinion);
How to split paired-end FASTQ files using seqkit?
Once you have the two files, you should order them to be sure that the reads are really paired. We can split FASTQ files using Seqkit. https://bioinf.shenwei.me/seqkit/usage/#split2 Example 4 will help this question.
Do you use regex for FASTQ file parsing?
Avoid using a regex for simple fastq file parsing if you can use line numbers, both for speed (pattern matching is slower than simple counting) and for robustness. Highly unlikely, but a pattern like ^@.*/1$ (or whatever the readers might change it to, while reusing this code later) can match also the base quality line.
How many FASTQ files are there in Illumina MiniSeq?
On an Illumina MiniSeq instrument, there can be up to 100M records in a single file. There are two FastQ files generated in an Illumina paired-end reads sequencing run. The files have this naming convention: Most downstream data analysis tools automatically recognize the fact that the R1 and R2 files are paired with one other.
How to split paired-end FASTQ files using grep?
Or online tools with Galaxy web UI, for example this tool: “FASTQ splitter on joined paired end reads”, installed on several public Galaxy instances, such as https://usegalaxy.org/ . Avoid using a regex for simple fastq file parsing if you can use line numbers, both for speed (pattern matching is slower than simple counting) and for robustness.
What kind of file is fastq.gz file?
All the generated output files are fastqsanger format. .fastqsanger is an uncompressed plain text formatting. Any plain text editor should be able to read the files. Those may not recognize the format by default since the file extension doesn’t end with a .txt – however, that is what this data is (at the most basic level).
Is the barcode splitter really producing fastq.gz?
The correct way is via the neighbouring Convert tab. That offers an option to decompress compressed fastq. The other way round is not offered though. Is the Barcode splitter really producing fastq, when you feed it fastq.gz datasets?