Preparation of reference
SAW provides two complementary pipelines, SAW makeRef and SAW checkGTF, for genome reference and annotation files.
Before running SAW count, one or more reference index files should be built in advance.
A complementary tool for genome reference builds index files needed by SAW count pipeline.
Because of the multiple uses of makeRef for three bioinformatical tools, --mode decides which one works.
Annotation files in the standard format can be accepted by SAW count. The verification will be performed automatically before read alignment in SAW count. In addition to the usual format check, the extraction of specific annotations is also implemented.
SAW accepts the annotation files suffix withgtf/gtf.gz, gff/gff.gz, gff3/gff3.gz.
Last updated