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 |