建库时是否是链特异性建库。
Tophat2:
| --library-type | The default is unstranded (fr-unstranded). If either fr-firststrand or fr-secondstrand is specified, every read alignment will have an XS attribute tag as explained below. Consider supplying library type options below to select the correct RNA-seq protocol. |
| Library Type | Examples | Description |
| fr-unstranded | Standard Illumina | Reads from the left-most end of the fragment (in transcript coordinates) map to the transcript strand, and the right-most end maps to the opposite strand. |
| fr-firststrand | dUTP, NSR, NNSR | Same as above except we enforce the rule that the right-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during first strand synthesis is sequenced. |
| fr-secondstrand | Ligation, Standard SOLiD | Same as above except we enforce the rule that the left-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during second strand synthesis is sequenced. |
HISAT2:--rna-strandness <string>
Specify strand-specific information: the default is unstranded.
For single-end reads, use F or R. ‘F‘ means a read corresponds to a transcript. ‘R‘ means a read corresponds to the reverse complemented counterpart of a transcript. For paired-end reads, use either FR or RF.
With this option being used, every read alignment will have an XS attribute tag: ‘+‘ means a read belongs to a transcript on ‘+‘ strand of genome. ‘-‘ means a read belongs to a transcript on ‘-‘ strand of genome.
library-type:fr-unstanded vs fisrt-stand vs second-stanrd
原文：http://www.cnblogs.com/timeisbiggestboss/p/7170087.html