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: [~12 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:

(
cd /home/train/Annotation_workshop/Augustus/Prediction/Chr3-1065466-1464870/run1
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: [~3 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/run2.log \
    --predictionStart=1065466 \
    --predictionEnd=1464870 \
    ../Inputs/Athaliana_447_TAIR10.Chr3.fa
)

2.2 Convert Augustus GTF into GFF3 format:

(
cd /home/train/Annotation_workshop/Augustus/Prediction/Chr3-1065466-1464870/run2
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: [~3 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 Augustus GTF into GFF3 format:

(
cd /home/train/Annotation_workshop/Augustus/Prediction/Chr3-1065466-1464870/run3
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: [~1 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 Augustus GTF into GFF3 format:

(
cd /home/train/Annotation_workshop/Augustus/Prediction/Chr3-1065466-1464870/run4
augustus_gtf_to_gff3 ARATH3702_run4 Output/run4.raw.gtf
)