Augustus
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How to recognise partial or complete genes
Hi, I used the following commands for Augustus. However, how can I recognise which genes Augustus has predicted as partial or complete?
#bam2augustus
bam2hints –intronsonly --in=${r1} --out=${r1}.intron-hints.gff
bam2wig $r1 > ${r1}.wig
cat ${r1}.wig | wig2hints.pl --width=10 --margin=10 --minthresh=2 --minscore=4 --prune=0.1 --src=W --type=ep --radius=4.5 --pri=4 --strand="." > ${r1}.ep-hints.gff
cat ${r1}.intron-hints.gff ${r1}.ep-hints.gff > ${r1}.hints.gff
#Augustus
cat extrinsic.cfg
[SOURCES]
M RM E W
exonpart 1 .992 M 1 1e+100 RM 1 1 E 1 1 W 1 1.005
intron 1 .34 M 1 1e+100 RM 1 1 E 1 1e5 W 1 1
CDSpart 1 1 0.985 M 1 1e+100 RM 1 1 E 1 1 W 1 1
UTRpart 1 1 0.985 M 1 1e+100 RM 1 1 E 1 1 W 1 1
nonexonpart 1 1 M 1 1e+100 RM 1 1.01 E 1 1 W 1 1
#augustus
augustus ${asm} --noInFrameStop=false --genemodel=complete --species=coyote_tobacco --gff3=on --UTR=on --extrinsicCfgFile=$3 --alternatives-from-sampling=false --alternatives-from-evidence=true --uniqueGeneId=true --hintsfile=${hints} --allow_hinted_splicesites=atac > ${2}/${output}.gff3
Thank you in advance,
Michal