Alignment module
Description
Scripts for evaluation of spliced aligners, written to assess RNA-seq mappers as part of the RGASP project.
License
If using this software, please cite: Engström et al. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods, in press.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of alignment and load default version of alignment as
module avail alignment/ # list available modules module load alignment # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail alignment
and choose explicit version you want to use.
Available perl scripts are (run any of the perl scripts without arguments to see a usage message briefly explaining what the script does and what command-line parameters can be used):
calc_sim_accuracy.pl cmp_alignment_and_cufflinks_gaps.pl count_intronic_aln.pl count_mm_binned.pl cufflinks_eval.pl gap_stats.pl get_gap_mm_pos.pl get_gene_types_from_gtf.pl adapt_sam_for_sim_eval.pl validate_bam.pl calc_indel_shift.pl filter_gtf_by_expr.pl get_junction_coverage.pl
Available R scripts are:
make_alignment_vs_cufflinks_gaps_tables.R make_multi-intron_accuracy_tables.R make_pair_ali_yield_table.R make_sim_eval_tables.R plot_gap_mm_pos.R plot_intron_known_vs_novel.R plot_sim_indel_accuracy.R plot_sim_intron_roc.R plot_sim_read_placement_bars.R plot_sim_splice_accuracy_scatter.R plot_sim_splice_recall_by_coverage.R
R scripts can be run via command (to use our own datasets, please set up RGASP_ALI_DATA variable before computation -- for more detailed explanation, see documentation):
R --no-save --no-restore < $RGASP_ALI_HOME/scripts/R/<script_name>
Documentation
https://github.com/RGASP-consortium/alignment/blob/master/doc/manual.md