Augustus Prediction

Augustus Prediction

1. Augustus Prediction - Run1

Augustus gene prediction run making use of all extrinsic evidence and weighted towards transcript assemblies along with RNA-Seq coverage

1.1 Start Augustus run: [~22 mins]

cd /home/train/Annotation_workshop/Augustus/Prediction/Chr3-1065466-1464870/run1
rm -rf Output && mkdir -p Output
/usr/bin/time -v augustus --AUGUSTUS_CONFIG_PATH=../Inputs/config --species=ath_wksp_opt --UTR=on --extrinsicCfgFile=../Inputs/extrinsic.ei_augustus340_generic.cfg --alternatives-from-evidence=true --hintsfile=hints/extrinsic.augustus.run1.gff3 --noInFrameStop=true --allow_hinted_splicesites=atac --outfile=Output/run1.raw.gtf --errfile=Output/run1.log --predictionStart=1065466 --predictionEnd=1464870 ../Inputs/Athaliana_447_TAIR10.Chr3.fa

1.2 Convert Augustus GTF into GFF3 format:

augustus_gtf_to_gff3 ARATH3702_run1 Output/run1.raw.gtf

2. Augustus Prediction - Run2

Augustus gene prediction run making use of all extrinsic evidence, same as run1, but without RNA-Seq coverage

2.1 Start Augustus run: [~5 mins]

cd /home/train/Annotation_workshop/Augustus/Prediction/Chr3-1065466-1464870/run2
rm -rf Output && mkdir -p Output
/usr/bin/time -v augustus --AUGUSTUS_CONFIG_PATH=../Inputs/config --species=ath_wksp_opt --UTR=on --extrinsicCfgFile=../Inputs/extrinsic.ei_augustus340_generic.cfg --alternatives-from-evidence=true --hintsfile=hints/extrinsic.augustus.run2.gff3 --noInFrameStop=true --allow_hinted_splicesites=atac --outfile=Output/run2.raw.gtf --errfile=Output/run1.log --predictionStart=1065466 --predictionEnd=1464870 ../Inputs/Athaliana_447_TAIR10.Chr3.fa

2.2 Convert Augsustus GTF into GFF3 format:

augustus_gtf_to_gff3 ARATH3702_run2 Output/run2.raw.gtf

3. Augustus Prediction - Run3

Augustus gene prediction run makes use of all extrinsic evidence, same as run2, but weighted towards protein alignments

3.1 Start Augustus run: [~5 mins]

cd /home/train/Annotation_workshop/Augustus/Prediction/Chr3-1065466-1464870/run3
rm -rf Output && mkdir -p Output
/usr/bin/time -v augustus --AUGUSTUS_CONFIG_PATH=../Inputs/config --species=ath_wksp_opt --UTR=on --extrinsicCfgFile=../Inputs/extrinsic.ei_augustus340_generic.cfg --alternatives-from-evidence=true --hintsfile=hints/extrinsic.augustus.run3.gff3 --noInFrameStop=true --allow_hinted_splicesites=atac --outfile=Output/run3.raw.gtf --errfile=Output/run3.log --predictionStart=1065466 --predictionEnd=1464870 ../Inputs/Athaliana_447_TAIR10.Chr3.fa

3.2 Convert Augsustus GTF into GFF3 format:

augustus_gtf_to_gff3 ARATH3702_run3 Output/run3.raw.gtf

4. Augustus Prediction - Run4

Ab initio Augustus gene prediction run without making use of any extrinsic evidence

4.1 Start Augustus run: [~2 mins]

cd /home/train/Annotation_workshop/Augustus/Prediction/Chr3-1065466-1464870/run4
rm -rf Output && mkdir -p Output
/usr/bin/time -v augustus --AUGUSTUS_CONFIG_PATH=../Inputs/config --species=ath_wksp_opt --UTR=on --noInFrameStop=true --allow_hinted_splicesites=atac --outfile=Output/run4.raw.gtf --errfile=Output/run4.log --predictionStart=1065466 --predictionEnd=1464870 ../Inputs/Athaliana_447_TAIR10.Chr3.fa

4.2 Convert Augsustus GTF into GFF3 format:

augustus_gtf_to_gff3 ARATH3702_run4 Output/run4.raw.gtf