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01_Circos_Figure_3.md

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Creation of circos figure showing duplication overlap with effectors/HGT

Circos plot to represent TE TD HGT and effector predictions

#/work/GIF/remkv6/Baum/CamTechGenomeComparison/58_Renamatorium/31_Fig3Circos
#Copied template karyotype.conf, ideogram.conf, bands.conf, and ticks.conf from Globodera rostochiensis synteny study
cp ../../26_GloboderaSynteny/otherGloboderaGenomes/rostochiensis/circos/* .

#remade the karyttype file so it is only scn
bioawk -c fastx '{print $name,length($seq)}' ../1_genomeNgff/genome738sl.polished.mitoFixed.fa |sort -k2,2nr |head -n 20 |awk '{print "chr","-",$1,$1,"0",$2}' >Top20Scaf.kary


#need to make a histogram or plot points.  I am going with histogram first to get a feel for the presentation
awk '{print $2}'  Top20Scaf.kary |while read line; do echo "awk '\$1==\""$line"\" && \$3==\"gene\"' ../1_genomeNgff/fixed.augustus.gff3 >>Genesoftop20scaffolds.gff" ;done >GetGenesoftop20scaffolds.sh
Genesoftop20scaffolds.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >Genes.histo

awk '{print $2}'  Top20Scaf.kary |while read line; do echo "awk '\$1==\""$line"\" ' ../27_TandemRedo/ >>Genesoftop20scaffolds.gff" ;done >GetGenesoftop20scaffolds.sh

#/work/GIF/remkv6/Baum/CamTechGenomeComparison/58_Renamatorium/30_BenNewHGT
less HighConfHGT.list |sed 's/\.t/\t/g'|cut -f 1 |sort|uniq|grep  -f - <(awk '$3=="gene"' ../1_genomeNgff/fixed.augustus.gff3|sed 's/;/\t/g') >HighConfHGT.gene.gff


#/work/GIF/remkv6/Baum/CamTechGenomeComparison/58_Renamatorium/31_Fig3Circos
 awk '{print $2}'  Top20Scaf.kary |while read line; do echo "awk '\$1==\""$line"\"' HighConfHGT.gene.gff >>HGTGenesoftop20scaffolds.gff" ;done >HGTGetGenesoftop20scaffolds.sh
 sh HGTGetGenesoftop20scaffolds.sh
less HGTGenesoftop20scaffolds.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >HGTGenes.histo


ln -s ../26_ExpressionSets/AllPredictedEffectors.list
less AllPredictedEffectors.list |grep  -f - <(awk '$3=="gene"' Genesoftop20scaffolds.gff|sed 's/;/\t/g') >AllPredictedEffectorsoftop20scaffolds.gff
less AllPredictedEffectorsoftop20scaffolds.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >AllPredictedEffectors.histo

ln -s ../23_LTR_finder/LtrRetroelementClassified.gff
awk '{print $2}'  Top20Scaf.kary |while read line; do echo "awk '\$1==\""$line"\"' LtrRetroelementClassified.gff >>LTRsoftop20scaffolds.gff" ;done >LTRsoftop20scaffolds.sh
less LTRsoftop20scaffolds.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >LTRsoftop20scaffolds.histo

ln -s ../24_IRF_DNATrans/SupportedIRFMergeClassified.gff
awk '{print $2}'  Top20Scaf.kary |while read line; do echo "awk '\$1==\""$line"\"' SupportedIRFMergeClassified.gff >>TIRsoftop20scaffolds.gff" ;done >TIRsoftop20scaffolds.sh
less TIRsoftop20scaffolds.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >TIRsoftop20scaffolds.histo

ln -s ../2_repeats/genome738sl.polished.mitoFixed.fa.out.gff
awk '{print $2}'  Top20Scaf.kary |while read line; do echo "awk '\$1==\""$line"\"' genome738sl.polished.mitoFixed.fa.out.gff >>Repeatsoftop20scaffolds.gff" ;done >Repeatsoftop20scaffolds.sh
less Repeatsoftop20scaffolds.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >Repeatsoftop20scaffolds.histo

ln -s ../27_TandemRedo/TotalSections.gff
awk '{print $2}'  Top20Scaf.kary |while read line; do echo "awk '\$1==\""$line"\"' TotalSections.gff >>TDRoftop20scaffolds.gff" ;done >TDRoftop20scaffolds.sh
less TDRoftop20scaffolds.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >TDRoftop20scaffolds.histo

these needed changed to heatmap, and were not very interesting for the top 20 largest scaffolds. decided to look at the scaffolds with the greatest numbers of duplications

awk '($5-$4)>2000 {print $1}' TotalSections.gff |sort|uniq -c |sort -k1,1nr |awk '{print $2}' |head |cdbyank ../1_genomeNgff/genome738sl.polished.mitoFixed.fa.cidx |bioawk -c fastx '{print "chr","-",$name,$name,"0",length($seq)}' >HighTDRTop10Scaffs.kary

less HighTDRTop10Scafs.kary|awk '{print $2}' |while read line; do echo "awk '\$1==\""$line"\" && \$3==\"gene\"' ../1_genomeNgff/fixed.augustus.gff3 >>HighTDRTopScaffs.gff";done >GetGenesofHighTDRTopScaffs.gff.sh
sh GetGenesofHighTDRTopScaffs.gff.sh

#reiteration of the first run to generate appropriate histo files
less HighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >Genes.histo
less HighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' |awk '{print $1,$2/100000,$3/100000}' |awk '{printf $1; printf "%16f", $2; printf "%17f\n", $3 }' |sed 's/\./\t/g' |awk '{print $1,$2*100000,($4*100000)+100000}' |sort|uniq -c |awk '{print $2,$3,$4,$1}'  >GenesEst.histo

awk '($5-$4)>2000 {print $1}' TotalSections.gff |sort|uniq -c |sort -k1,1nr |awk '{print $2}' |head |grep  -f - <(awk '$3=="gene"' HighTDRTopScaffs.gff|sed 's/;/\t/g') >AllPredictedEffectorsofHighTDRTopScaffs.gff
less HighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >AllPredictedEffectors.histo

 awk '($5-$4)>2000 {print $1}' TotalSections.gff |sort|uniq -c |sort -k1,1nr |awk '{print $2}' |head|while read line; do echo "awk '\$1==\""$line"\"' HighConfHGT.gene.gff >>HGTGenesofHighTDRTopScaffs.gff" ;done >HGTGetGenesofHighTDRTopScaffs.sh
 sh HGTGetGenesofHighTDRTopScaffs.sh
less HGTGenesofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >HGTGenesofHighTDRTopScaffs.histo

less AllPredictedEffectors.list |grep  -f - <(awk '$3=="gene"' HighTDRTopScaffs.gff|sed 's/;/\t/g') >AllPredictedEffectorsofHighTDRTopScaffs.gff
less AllPredictedEffectorsofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >AllPredictedEffectorsHighTDRTopScaffs.histo


#ln -s ../23_LTR_finder/LtrRetroelementClassified.gff
awk '($5-$4)>2000 {print $1}' TotalSections.gff |sort|uniq -c |sort -k1,1nr |awk '{print $2}' |head|while read line; do echo "awk '\$1==\""$line"\"' LtrRetroelementClassified.gff >>LTRsofHighTDRTopScaffs.gff" ;done >LTRsofHighTDRTopScaffs.sh
sh LTRsofHighTDRTopScaffs.sh
less LTRsofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >LTRsofHighTDRTopScaffs.histo

ln -s ../24_IRF_DNATrans/SupportedIRFMergeClassified.gff
awk '($5-$4)>2000 {print $1}' TotalSections.gff |sort|uniq -c |sort -k1,1nr |awk '{print $2}' |head |while read line; do echo "awk '\$1==\""$line"\"' SupportedIRFMergeClassified.gff >>TIRsofHighTDRTopScaffs.gff" ;done >TIRsofHighTDRTopScaffs.gff.sh
sh TIRsofHighTDRTopScaffs.gff.sh
less TIRsofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >TIRsHighTDRTopScaffs.histo

ln -s ../2_repeats/genome738sl.polished.mitoFixed.fa.out.gff
awk '($5-$4)>2000 {print $1}' TotalSections.gff |sort|uniq -c |sort -k1,1nr |awk '{print $2}' |head |while read line; do echo "awk '\$1==\""$line"\"' genome738sl.polished.mitoFixed.fa.out.gff >>RepeatsofHighTDRTopScaffs.gff" ;done >RepeatsHighTDRTopScaffs.sh
sh Repeatsoftop20scaffolds.sh
less RepeatsofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >RepeatsofHighTDRTopScaffs.histo
less RepeatsofHighTDRTopScaffs.histo |awk '{print $1,$2/100000,$3/100000}' |awk '{printf $1; printf "%16f", $2; printf "%17f\n", $3 }'|sed 's/\./\t/g' |awk '{print $1,$2*100000,($4*100000)+100000}' |sort |uniq -c |sort -k1,1nr |awk '{print $2,$3,$4,$1}' >RepeatEst.histo
ln -s ../27_TandemRedo/TotalSections.gff
awk '($5-$4)>2000 {print $1}' TotalSections.gff |sort|uniq -c |sort -k1,1nr |awk '{print $2}' |head |while read line; do echo "awk '\$1==\""$line"\"' TotalSections.gff >>TDRofHighTDRTopScaffs.gff" ;done >TDRofHighTDRTopScaffs.sh
sh TDRofHighTDRTopScaffs.sh
less TDRofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >TDRofHighTDRTopScaffs.histo

Figured out what needed displayed here, effecotr/hgt overlap with duplicative tracks. So grabbign top ten scaffolds from this list and repeating above analysis

cat ../26_ExpressionSets/AllPredictedEffectors.list ../26_ExpressionSets/HGTRevised.list |sort|uniq|cat  - <(cat ../26_ExpressionSets/SupportedIRFMergeClassified.list ../26_ExpressionSets/NonRedundantLtrRetroelementMerge.list ../26_ExpressionSets/tandem.gene.list |sort|uniq) |sort|uniq -c |awk '$1==2' |awk '{print $2}' |grep -w -f - <(sed 's/;/\t/g' ../1_genomeNgff/fixed.augustus.gff3 ) |awk '$3=="gene"' |awk '{print $1}' |sort|uniq -c |sort -k1,1nr |head |awk '{print $2}' >TopScaffoldsofEffHGToverlappingTIRLTRTDR.list


module load bioawk
module load cdbfasta
less TopScaffoldsofEffHGToverlappingTIRLTRTDR.list |cdbyank ../1_genomeNgff/genome738sl.polished.mitoFixed.fa.cidx |bioawk -c fastx '{print "chr","-",$name,$name,"0",length($seq),"green"}' >HighTDRTop10Scaffs.kary

less HighTDRTop10Scaffs.kary|awk '{print $3}' |while read line; do echo "awk '\$1==\""$line"\" && \$3==\"gene\"' ../1_genomeNgff/fixed.augustus.gff3 >>HighTDRTopScaffs.gff";done >GetGenesofHighTDRTopScaffs.gff.sh
sh GetGenesofHighTDRTopScaffs.gff.sh

reiteration of the first run to generate appropriate histo files

less HighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >Genes.histo
less HighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' |awk '{print $1,$2/100000,$3/100000}' |awk '{printf $1; printf "%16f", $2; printf "%17f\n", $3 }' |sed 's/\./\t/g' |awk '{print $1,$2*100000,($4*100000)+100000}' |sort|uniq -c |awk '{print $2,$3,$4,$1}'  >GenesEst.histo

less TopScaffoldsofEffHGToverlappingTIRLTRTDR.list |grep  -f - <(awk '$3=="gene"' HighTDRTopScaffs.gff|sed 's/;/\t/g') >AllPredictedEffectorsofHighTDRTopScaffs.gff
less HighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >AllPredictedEffectors.histo

less TopScaffoldsofEffHGToverlappingTIRLTRTDR.list|while read line; do echo "awk '\$1==\""$line"\"' HighConfHGT.gene.gff >>HGTGenesofHighTDRTopScaffs.gff" ;done >HGTGetGenesofHighTDRTopScaffs.sh
 sh HGTGetGenesofHighTDRTopScaffs.sh
less HGTGenesofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >HGTGenesofHighTDRTopScaffs.histo

less AllPredictedEffectors.list |grep  -f - <(awk '$3=="gene"' HighTDRTopScaffs.gff|sed 's/;/\t/g') >AllPredictedEffectorsofHighTDRTopScaffs.gff
less AllPredictedEffectorsofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >AllPredictedEffectorsHighTDRTopScaffs.histo


#ln -s ../23_LTR_finder/LtrRetroelementClassified.gff
less TopScaffoldsofEffHGToverlappingTIRLTRTDR.list|while read line; do echo "awk '\$1==\""$line"\"' LtrRetroelementClassified.gff >>LTRsofHighTDRTopScaffs.gff" ;done >LTRsofHighTDRTopScaffs.sh
sh LTRsofHighTDRTopScaffs.sh
less LTRsofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >LTRsofHighTDRTopScaffs.histo
q
ln -s ../24_IRF_DNATrans/SupportedIRFMergeClassified.gff
less TopScaffoldsofEffHGToverlappingTIRLTRTDR.list |while read line; do echo "awk '\$1==\""$line"\"' SupportedIRFMergeClassified.gff >>TIRsofHighTDRTopScaffs.gff" ;done >TIRsofHighTDRTopScaffs.gff.sh
sh TIRsofHighTDRTopScaffs.gff.sh
less TIRsofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >TIRsHighTDRTopScaffs.histo

ln -s ../2_repeats/genome738sl.polished.mitoFixed.fa.out.gff
less TopScaffoldsofEffHGToverlappingTIRLTRTDR.list |while read line; do echo "awk '\$1==\""$line"\"' genome738sl.polished.mitoFixed.fa.out.gff >>RepeatsofHighTDRTopScaffs.gff" ;done >RepeatsHighTDRTopScaffs.sh
sh RepeatsHighTDRTopScaffs.sh
less RepeatsofHighTDRTopScaffs.gff|awk '{print $1"\t"$4"\t"$5"\t100"}' >RepeatsofHighTDRTopScaffs.histo
less RepeatsofHighTDRTopScaffs.histo |awk '{print $1,$2/100000,$3/100000}' |awk '{printf $1; printf "%16f", $2; printf "%17f\n", $3 }'|sed 's/\./\t/g' |awk '{print $1,$2*100000,($4*100000)+100000}' |sort |uniq -c |sort -k1,1nr |awk '{print $2,$3,$4,$1}' >RepeatEst.histo
ln -s ../27_TandemRedo/TotalSections.gff
less TopScaffoldsofEffHGToverlappingTIRLTRTDR.list |while read line; do echo "awk '\$1==\""$line"\"' redTandemAll.bed >>TDRofHighTDRTopScaffs.bed" ;done >TDRofHighTDRTopScaffs.sh
sh TDRofHighTDRTopScaffs.sh
cp TDRofHighTDRTopScaffs.bed TDRofHighTDRTopScaffs.histo

circosPlot