Alignment module

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Description

Scripts for evaluation of spliced aligners, written to assess RNA-seq mappers as part of the RGASP project.

Category

Aligners

Licence

If using this software, please cite: Engström et al. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods, in press.

Use

module add alignment #this command adds several scripts to PATH

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

Homepage

https://github.com/RGASP-consortium/alignment

Program manager

meta@cesnet.cz