sampleR1fastqgz

sampleR1.fastq.gz is a gzipped FASTQ file that contains sequencing reads for Read 1 (R1) from a single sample in a paired-end sequencing experiment. In Illumina and other platforms, sequencing produces two reads per DNA fragment: Read 1 and Read 2. The R1 file stores the first read sequences with their corresponding base quality scores, encoded in the FASTQ format. The file is compressed with gzip to reduce storage requirements and to facilitate transfer.

A FASTQ entry consists of four lines: a header with an identifier, the nucleotide sequence, a plus sign, and a line of ASCII quality scores. Multiple entries are concatenated to form the complete file. In a paired-end run, there is typically a corresponding sampleR2.fastq.gz for Read 2, named to align with the R1 file.

Naming conventions vary; the R1 suffix signals Read 1, while R2 would indicate Read 2. Pipelines often assume matching R1 and R2 files for each sample, and metadata or a manifest links these files to sample IDs, lanes, and sample treatments.

Common uses include quality assessment with FastQC, adapter and quality trimming with tools like fastp or Trimmomatic, and downstream alignment and variant calling with BWA, Bowtie2, or pipelines such as GATK. Handling gzipped FASTQ files directly is supported by most modern bioinformatics tools, though some steps may decompress them temporarily.