Appendix A - Sequence file naming pattern

RNA-seq Analysis Portalsupports analysis of FASTQ files generated by Illumina, Element Biosciences, and MGI sequencers, and BAM files from Thermo Fisher Ion Torrent sequencers.

To ensure FASTQ files are grouped correctly into samples during upload, sequence file names must follow the supported naming conventions described below.

If you have FASTQ files from a Thermo Fisher Ion Torrent sequencer, you may manually rename them to match the supported patterns.

Illumina, and Element Biosciences (legacy naming)

Single-lane, paired-end example

Two FASTQ files grouped into one sample (TC-35-A_S1): 

	TC-35-A_S1_L001_R1_001.fastq.gz
	TC-35-A_S1_L001_R2_001.fastq.gz

Four-lane, paired-end data

Eight FASTQ files grouped into one sample (501-708-SEQC-77-1_S1): 

	501-708-SEQC-77-1_S1_L001_R1_001.fastq.gz
	501-708-SEQC-77-1_S1_L001_R2_001.fastq.gz
	501-708-SEQC-77-1_S1_L002_R1_001.fastq.gz
	501-708-SEQC-77-1_S1_L002_R2_001.fastq.gz
	501-708-SEQC-77-1_S1_L003_R1_001.fastq.gz
	501-708-SEQC-77-1_S1_L003_R2_001.fastq.gz
	501-708-SEQC-77-1_S1_L004_R1_001.fastq.gz
	501-708-SEQC-77-1_S1_L004_R2_001.fastq.gz

Single-lane, single-read data

Each file represents a separate sample: 

	QL4_S4_L001_R1_001.fastq
	QL6_S6_L001_R1_001.fastq

Imported samples: QL4_S4 and QL6_S6

Element Biosciences (default naming)

File names may be with or without "R".

Single-lane, paired-end data

Two FASTQ files grouped into one sample (Sample28): 

	Sample28_R1.fastq.gz
	Sample28_R2.fastq.gz

MGI

File names may be with or without "R".

Single-lane, paired-end data

Two FASTQ files grouped into one sample (Sample49): 

	Sample49_L01_R1_001.fastq.gz
	Sample49_L01_R2_001.fastq.gz