Fragment library types

RNA-seq library preparation protocols differ in ways that matter for quantification: reads can be single-end or paired-end, the protocol can be unstranded or strand-specific, and paired-end reads have a relative orientation. salmon describes all of these with a short library-type string passed to -l/--libType.

Just use -l A

If you are unsure, pass -l A and salmon will automatically detect the library type from the data. The explicit codes below are for when you want to fix it.

The library-type string has up to three parts: relative orientation, strandedness, and directionality.

1. Relative orientation (paired-end only)

Code	Meaning
I	Inward — mates point toward each other
O	Outward — mates point away from each other
M	Matching — mates point the same way

2. Strandedness

Code	Meaning
S	Stranded (strand-specific protocol)
U	Unstranded

If the protocol is unstranded (U), the string ends here.

3. Directionality (stranded protocols only)

Code	Meaning
F	Read 1 (or the single-end read) comes from the forward strand
R	Read 1 (or the single-end read) comes from the reverse strand

Examples

String	Interpretation
IU	Unstranded paired-end, mates face each other
ISF	Stranded paired-end, inward, read 1 from the forward strand
OSR	Stranded paired-end, outward, read 1 from the reverse strand
U	Unstranded single-end
SF	Stranded single-end, reads from the forward strand
SR	Stranded single-end, reads from the reverse strand

Single-end libraries omit the orientation part, so the only valid single-end strings are U, SF, and SR.

Correspondence to TopHat library types

TopHat	salmon (paired-end)	salmon (single-end)
-fr-unstranded	-l IU	-l U
-fr-firststrand	-l ISR	-l SR
-fr-secondstrand	-l ISF	-l SF

The remaining salmon library strings have no direct TopHat equivalent.