Salmon之Fragment Library Types

library类型

SAM file flags：https://biobeat.wordpress.com/2013/04/29/directional-rna-seq-part-1-extract-strand-information-from-sam-file/

library类型可以分解为三个部分：reads的相对方向，library的链型和reads的方向性。如下图所示：

reads的相对方向

I = inward
O = outward
M = matching

library的链型

S = stranded
U = unstranded

reads的方向性

注意：此项的应用前提是：建库时采用的是strand-specific步骤。

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

实例

IU 
### an unstranded paired-end library where the reads face each other

SF
### a stranded single-end protocol where the reads come from the forward strand

OSR 
### a stranded paired-end protocol where the reads face away from each other,
### read1 comes from reverse strand and read2 comes from the forward strand

与TopHat library类型的对应关系

TopHat	Salmon (and Sailfish)
	Paired-end	Single-end
-fr-unstranded	-l IU	-l U
-fr-firststrand	-l ISR	-l SR
-fr-secondstrand	-l ISF	-l SF