SCRIPTURE¶

Description¶

Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

Note: export _JAVA_OPTIONS="-Xmx?g" where ? equals to the available memory.

Environment Modules¶

Run module spider scripture to find out what environment modules are available for this application.

Environment Variables¶

HPC_SCRIPTURE_DIR - installation directory
HPC_SCRIPTURE_BIN - executable directory
HPC_SCRIPTURE_LIB - library directory

Citation¶

If you publish research that uses scripture you have to cite it as follows:

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs https://doi.org/10.1038/nbt.1633

Categories¶

biology, genomics