TrUC

Transcription Units by Coverage

Description

Install

An installation example is provided at the end of the user manual, as well as in the "INSTALL" file. Once all the dependencies are installed, use the "check" file to make sure everything is ok.

 ./check

Usage

To run TrUC use the following command

truc (version 1.00) [MODE] : Transcription Units by Coverage
 TSS : Predict Transcription Start Sites (Need CapSeq mapping)
 TTS : Predict Transcription Terminal Site (polyA mRNA sequencing)
 Transcript : Predict Transcription Units
 UTR : Add UTRs to a GFF3 file
 Intron : Predict Introns

License

This software is distributed under the GNU GPL v3 license. See the "LICENSE" file for details.

How to cite

If you use this software please cite the following publication

Olivier Arnaiz, Erwin Van Dijk, Mireille Bétermier, Maoussi Lhuillier-Akakpo, Augustin De Vannsay, Sandra Duharcourt, Erika Sallet, Jérôme Gouzy and Linda Sperling Improved methods and resources for Paramecium genomics: Transcription Units, Gene Annotation and Gene Expression. Submited

Example

The example directory contains the following files :

example/reference.fa : A refence sequence example/CapSeq.bam : 5'CapSeq data example/mRNAseq.bam : mRNA seq data example/mRNAseq_partial_mapping.bam : mRNA seq data allowing partial mapping example/annotation.gff3 : GFF3 annotation file

TSS : Predict Transcription Start Sites (Need CapSeq mapping)

OUT_DIR=TEST
THREADS=6
MIN_COVERAGE=15
MIN_SCORE=15

./truc TSS -v -genome example/reference.fa -out_dir $OUT_DIR -threads $THREADS -min_coverage $MIN_COVERAGE -min_score $MIN_SCORE -bam example/CapSeq.bam

TTS : Predict Transcription Terminal Site (polyA mRNA sequencing)

OUT_DIR=TEST
THREADS=6
MIN_COVERAGE=5
MIN_SCORE=10
NB_MIN_A=5

./truc TTS -v -genome example/reference.fa -out_dir $OUT_DIR -threads $THREADS -min_coverage $MIN_COVERAGE -min_score $MIN_SCORE -nb_min_A $NB_MIN_A -bam example/mRNAseq_partial_mapping.bam

Intron : Predict introns

OUT_DIR=TEST
THREADS=6
MIN_COVERAGE=5
MIN_SCORE=10
MIN_INTRON=15
MAX_INTRON=100
MIN_INTRON_COVERAGE=15
MIN_SPLICING_RATE=0.7

./truc Intron -v -genome example/reference.fa -out_dir $OUT_DIR -threads $THREADS -min_coverage $MIN_COVERAGE -min_score $MIN_SCORE -intron_consensus -min_intron_length $MIN_INTRON -max_intron_length $MAX_INTRON -min_intron_coverage $MIN_INTRON_COVERAGE -bam example/mRNAseq.bam

UTR : Add UTRs to a GFF3 file

OUT_DIR=TEST
THREADS=6
MIN_COVERAGE=5
MIN_SCORE=10
ANNOTATION=example/annotation.gff3

./truc UTR -v -genome example/reference.fa -out_dir $OUT_DIR -threads $THREADS -min_coverage $MIN_COVERAGE -min_score $MIN_SCORE -annotation $ANNOTATION -bam example/mRNAseq.bam

Transcript : Predict Transcription Units

OUT_DIR=TEST
THREADS=6
MIN_COVERAGE=5
MIN_SCORE=10
MIN_LENGTH=300
MIN_INTRON=15
MAX_INTRON=100
MIN_INTRON_COVERAGE=15
MIN_SPLICING_RATE=0.7
TSS=$OUT_DIR/transcription_start_site.gff3
TTS=$OUT_DIR/transcription_end_site.gff3

./truc Transcript -v -genome example/reference.fa -out_dir $OUT_DIR -threads $THREADS -min_coverage $MIN_COVERAGE -min_score $MIN_SCORE -min_length $MIN_LENGTH \
 -intron_consensus -min_intron_length $MIN_INTRON -max_intron_length $MAX_INTRON -min_intron_coverage $MIN_INTRON_COVERAGE \
 -no_overlap -tss $TSS -tts $TTS \
 -bam example/mRNAseq.bam