=======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	|NONE
^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|