Scallop Parameter Advising

This repo contains a wrapper for the Scallop transcriptome assembly tool.

installation

The wrapper is written in perl but requires an installation of the following applications:

• Scallop
• gffcompare
• rnaseqtools

If scallop, gffcompare and gtfcuff are not in your path they can be specified on the command line using the flags --scallop_path, -gffcompare_path and --gtfcuff_path respectively.

usage

The script ScallopAdvising.pl requires that the following options be given:

• --working_dir -- a folder in which temporary files will be stored
• --input_bam -- the mapping of RNA-seq reads to the reference genome
• --output_gtf -- the output file
• --reference -- the reference transcriptome corresponding to the reference genome used

Then a list of configuration files should be supplied (as described below). An example of the full command is

./ScallopAdvising.pl --working_dir temp/ --input_bam in.bam --output_gtf out.gtf --reference ref.gtf default.config config1.config

optionally the --log_file parameter can be used to output a TSV file that lists the AUC for each of the input configurations.

config files

The configuration files are flat files on which each line contains one tunable parameter and its corresponding value. Non-specified tunable parameters retain the default value.

An example of the default parameter configuration would be:

max_dp_table_size                   10000
max_edit_distance                   10
max_intron_contamination_coverage   2.0
max_num_exons                       1000
min_bundle_gap                      50
min_exon_length                     20
min_flank_length                    3
min_mapping_quality                 1
min_num_hits_in_bundle              20
min_router_count                    1
min_splice_boundary_hits            1
min_subregion_gap                   3
min_subregion_length                15
min_subregion_overlap               1.5
min_transcript_length_base          150
min_transcript_length_increase      50
uniquely_mapped_only                0
use_second_alignment                0

Paper Results

Information about how to obtain the data used for validating parameter advising for transcript assembly can be found in the publication_results/ directory. There you will find links and scripts to help retreive the necesary input to recreate the results found in the manuscript.

#Training

The information found in the training/ folder can be used to retrain either of the advisor set for a new set of data (though not neccesary).