-alignment: Path to the a spliced read alignment file. In this first version only one alignment is supported, so various sequencing lanes must be combined before invoking scripture. Alignments must be in BAM or SAM format and need to be both sorted and indexed. To sort and index we recommend to use igvtools (for SAM) and samtools (from BAM).
-sizeFile:A 2-column tab separated file containing the chromosome name and size for the organism.
-out: Output file name. The output contains a row per each of the records in the original file with 7 extra columns:
FWER corrected p-value for the observed read count across the transcript
Enrichment (i.e. observed # of reads / expected numbers of reads for transcript length) total number of reads across transcript
total reads across transcript
RPKM: number of reads which map per kilobase of exon model per million mapped reads for each gene, for each chromosome
local lambda, that is reads/base accross transcript genomic loci rather than spliced transcript
-sizeFile: A 2-column tab separated file containing the chromosome name and size for the organism.