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Highly_expressed_genes
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Highly_expressed_genes
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# Quantification of gene model expression
Expression was determined for aligned reads against predcited gene models using
cufflinks:
```bash
qlogin
Path=/home/groups/harrisonlab/project_files/verticillium_dahliae/pathogenomics
cd $Path
for Alignment in $(ls alignment/repeat_masked/12008*_accurate/accepted_hits.bam); do
Gff=gene_pred/codingquary1/V.dahliae/12008/final/final_genes_appended.gff3
OutDir=$(dirname $Alignment)
mkdir -p $OutDir/fpkm
ProgDir=/home/fanron/git_repos/tools/seq_tools/RNAseq
# qsub $ProgDir/sub4_cufflinks.sh $Gff $Alignment
cufflinks -p 8 -o $OutDir/fpkm -G $Gff $Alignment
done
```
fpkm_files=$(ls alignment/repeat_masked/12008PDA_accurate/fpkm/genes.fpkm_tracking | sed -r 's/\n/ /g')
ProgDir=/home/armita/git_repos/emr_repos/scripts/fusarium/RNAseq
Cazy=gene_pred/CAZY/*/*/*_CAZY_secreted_headers.txt
EffectorP=analysis/effectorP/*/*/*_EffectorP_secreted_headers.txt
mkdir analysis/expression
$ProgDir/fpkm_by_gene.py --fpkm_file $fpkm_files --CAZY_headers $Cazy --effectorP_headers $EffectorP > analysis/expression/12008_PDA_expressed_genes.tsv
fpkm_files=$(ls alignment/repeat_masked/12008CD_accurate/fpkm/genes.fpkm_tracking | sed -r 's/\n/ /g')
ProgDir=/home/armita/git_repos/emr_repos/scripts/fusarium/RNAseq
Cazy=gene_pred/CAZY/*/*/*_CAZY_secreted_headers.txt
EffectorP=analysis/effectorP/*/*/*_EffectorP_secreted_headers.txt
mkdir analysis/expression
$ProgDir/fpkm_by_gene.py --fpkm_file $fpkm_files --CAZY_headers $Cazy --effectorP_headers $EffectorP > analysis/expression/12008_CD_expressed_genes.tsv
*
echo "Number of variaible core genes in top 50 expressed genes:"
cat analysis/expression/12008_CD_expressed_genes.tsv | head -n 50 | grep -w -v -e 'contig_10_pilon' -e 'contig_14_pilon' -e 'contig_16_pilon' -e 'contig_18_pilon' -e 'contig_19_pilon' -e 'contig_20_pilon' -e 'contig_21_pilon' | grep -w -e 'contig_9_pilon' -e 'contig_11_pilon' -e 'contig_12_pilon' -e 'contig_13_pilon' -e 'contig_15_pilon' -e 'contig_17_pilon' | wc -l