quant

Quantification of secondary structures using EFastD/S files

Command line options for rsq quantify

usage: rsq quantify [-h] -d sce_genes.fd -s sce_genes.fs [-i sce_genes.isf]
                    [-e sce_genes.eprs] [-m 100] [-t 1e-6] [-o out.txt]

Program: rsq quantify (Quantify RNA structures given RNA footprinting data in
FastD format.)
optional arguments:
  -h, --help            show this help message and exit
Input options:
  -d sce_genes.fd, --fdfile sce_genes.fd
                        RNA footprinting data in FastD format.
  -s sce_genes.fs, --fsfile sce_genes.fs
                        RNA structure in FastS format.
  -i sce_genes.isf, --isoform sce_genes.isf
                        Transcript isoform information. Required only when
                        isoforms are considered.
  -e sce_genes.eprs, --expression sce_genes.eprs
                        Expression levels from gene expression data. Effective
                        only in isoform case. Format for each line:
                        geneid\isoform1\tRPKM\tisoform2\tRPKM\t...
  -m 100, --maxiter 100
                        Maximum number of iteration for EM algorithm. Default
                        is 100.
  -t 1e-6, --threshold 1e-6
                        Threshold for EM algorithm termination.
Output:
  -o out.txt, --outfile out.txt
                        Quantification output file.

Examples

Given the (extended) FastD and FastS file generated in the previous steps, run

>rsq quantify -d demo.efd -s demo.efs -o demo.txt

Output:

geneID  Percentages     loop_reads      stem_reads
YOR369C 0.398;0.602     257.077;451.713 169.087;192.254