RNAseq 文库类型与软件对应关系

Tool	RF/fr-firststrand stranded (dUTP)	FR/fr-secondstrand stranded (Ligation)	Unstranded
check_strandedness (output)	RF/fr-firststrand	FR/fr-secondstrand	unstranded
IGV (5p to 3p read orientation code)	F2R1	F1R2	F2R1 or F1R2
TopHat (–library-type parameter)	fr-firststrand	fr-secondstrand	fr-unstranded
HISAT2 (–rna-strandness parameter)	R/RF	F/FR
HTSeq (–stranded/-s parameter)	reverse	yes	no
STAR	n/a (STAR doesn’t use library strandedness info for mapping)	NONE	NONE
Picard CollectRnaSeqMetrics (STRAND_SPECIFICITY parameter)	SECOND_READ_TRANSCRIPTION_STRAND	FIRST_READ_TRANSCRIPTION_STRAND	NONE
Kallisto quant (parameter)	–rf-stranded	–fr-stranded	NONE
StringTie (parameter)	–rf	–fr	NONE
FeatureCounts (-s parameter)	2	1	0
RSEM (–forward-prob parameter)	0	1	0.5
Salmon (–libType parameter)	ISR (assuming paired-end with inward read orientation)	ISF (assuming paired-end with inward read orientation)	IU (assuming paired-end with inward read orientation)
Trinity (–SS_lib_type parameter)	RF	FR	NONE
MGI CWL YAML (strand parameter)	first	second	NONE
RegTools (strand parameter)	-s 1	-s 2	-s 0
	Example methods/kits: dUTP, NSR, NNSR, Illumina TruSeq Strand Specific Total RNA, NEBNext Ultra II Directional	Example methods/kits: Ligation, Standard SOLiD, NuGEN Encore, 10X 5’ scRNA data	Example kits/data: Standard Illumina, NuGEN OvationV2, SMARTer universal low input RNA kit (TaKara), GDC normalized TCGA data

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