Example Read Structures for BAM <-> FASTQ

This README shows a number of example datasets and their read structures for hts-specs#270.

Required Background

See Read Structures.

Note: Additional operators may be used below beyond [TBMS], for example C for cell-partition identifiers, to denote read segments that map into platform specific tags (for example C can map into the CR tag for 10x cell-partitioned data).

Note: if a sample barcode or molecular identifier is extracted from multiple reads, the bases are typically concatenated with a dash (-) delimiter.

Dual-Index Fragment Run

FASTQ	Description	Read Structure	SEQ/Tags
i1.fq	index/i7	+B	BC
i2.fq	index/i5	+B	BC
r1.fq	read-one/R1	+T	SEQ

Example technology:: Illumina Standard

Dual-Index Paired-End Run

FASTQ	Description	Read Structure	SEQ/Tags
i1.fq	index/i7	+B	BC
i2.fq	index/i5	+B	BC
r1.fq	read-one/R1	+T	SEQ
r2.fq	read-two/R2	+T	SEQ

Example technology:: Illumina Standard

Paired-End Run In-Line Sample Barcode

FASTQ	Description	Read Structure	SEQ/Tags
r1.fq	read-one/R1	10B+T*	BC and SEQ
r2.fq	read-two/R2	+T	SEQ

• example has 10 bases of sample barcode in read-one

Example technology: Missing

Paired-End Run i7 Sample Barcode and i5 Unique Molecular Identifier

FASTQ	Description	Read Structure	SEQ/Tags
i1.fq	index/i7	+B	BC
i2.fq	index/i5	+M	RX
r1.fq	read-one/R1	+T	SEQ
r2.fq	read-two/R2	+T	SEQ

• example has 10 bases of sample barcode in read-one

Example technology: NEBNext Direct

Paired-End Run In-Line and i7 Sample Barcode with In-line UMIs

FASTQ	Description	Read Structure	SEQ/Tags
i1.fq	index/i7	+B	BC
r1.fq	read-one/R1	8B8M+T	BC, RX, and SEQ
r2.fq	read-two/R2	8M+T	RX and SEQ

Example technology: Riptide™ High Throughput Rapid Library Prep (HT-RLP)

Dual-Index Paired-End Run with In-line Unique Molecular Identifiers and Skipped Bases

FASTQ	Description	Read Structure	SEQ/Tags
i1.fq	index/i7	+B	BC
i2.fq	index/i5	+B	BC
r1.fq	read-one/R1	8M1S+T	RX, Discarded, SEQ
r2.fq	read-two/R2	8M1S+T	RX, Discarded, SEQ

This is a good example of bases that are discarded and not present in the BAM

Example technology: TwinStrand Biosciences Duplex Sequencing

Single-Index Paired-End with In-line Cell Partition Identifiers and In-line Unique Molecular Identifiers and Skipped Bases

FASTQ	Description	Read Structure	SEQ/Tags
i1.fq	index/i7	+B	BC
r1.fq	read-one/R1	16C10M+S	CR, UR, TR(unused)
r2.fq	read-two/R2	+T	SEQ

Example technology: 10X Genomics Chromium Single Cell 3’ v2 Libraries (and BAM tags).

Dual-Index Providing Cell Partition Identifiers and Sample Identifiers, Paired-End with In-line Unique Molecular Identifiers

FASTQ	Description	Read Structure	SEQ/Tags
i1.fq	index/i7	+C	CR
i2.fq	index/i5	+B	BC
r1.fq	read-one/R1	+T	SEQ
r2.fq	read-two/R2	+M	UR

Example technology: 10X Genomics Chromium Single Cell 3’ v1 Libraries (driving bcl2fastq)