We recommend you first align your reads with MapSplice. Please refer to user guide for instructions on using MultiSplice.

Tips before using:

1. Please make sure the input annotation file is in GFF format;

2. Please make sure the read alignment file is in SAM format.

3. MultiSplice only works on single-end reads. In case of paired-end reads, please use MapPER to infer the transcript fragment first.

Source code and directory:

Latest version: