tophat

 

-g/--max-multihits <int>

Instructs TopHat to allow up to this many alignments to the reference   for a given read, and choose the alignments based on their alignment scores if there are more than this number.   The default is 20 for read mapping.  Unless you use --report-secondary-alignments, TopHat will report the alignments with the best alignment score.   If there are more alignments with the same score than this number, TopHat will randomly report only this many alignments.   In case of using --report-secondary-alignments, TopHat will try to report alignments up to this option value, and TopHat may randomly output some of the alignments with the same score to meet this number.

--report-secondary-alignments

By default TopHat reports best or primary alignments based on alignment scores (AS). Use this option if you want to output additional or secondary alignments  (up to 20 alignments will be reported this way, this limit can be changed by using the -g/--max-multihits option above).

 

               

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. (如果是链特异性的就要在tophat里加入这个参数，链特异性：建库时用试剂抹掉参考基因组中的一个链，只让reads比对到参考基因组中剩下的一条链。)
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.

 使用：--library-type=fr-firststrand

 

-i:

max deletion length (default 3) can not be equal to or greater than the min_intron_length.所以在设 -i 时候其值要大于3。