| 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 |