featureCounts

常用參數(shù)

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## 定義輸入輸出文件夾
trainee2/Nov10/project/Human_16-Asthma-Trans/Expression

gtf=/trainee2/Nov10//database/genome/Ensembl/Homo_sapiens/GRCh38_release95/Homo_sapiens.GRCh38.95.gtf.gz
inputdir=/trainee2/Nov10/project/Human_16-Asthma-Trans/Mapping/Hisat2
outputdir=/trainee2/Nov10/project/Human_16-Asthma-Trans/Expression/featureCount

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# featureCounts對bam文件進(jìn)行計數(shù)
featureCounts -T 5 -p -t exon -g gene_id -a $gtf -o all.id.txt $inputdir/*.sorted.bam

# 對定量結(jié)果質(zhì)控
multiqc all.id.txt.summary

# 得到表達(dá)矩陣
cat all.id.txt | cut -f1,7- > counts.txt

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salmon定量————不需要比對直接得到參考基因組表達(dá)

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# 構(gòu)建salmon索引
time salmon index -t Homo_sapiens.GRCh38.cdna.all.fa.gz -i Homo_sapiens.GRCh38.cdna.all.salmon

# 定義文件夾
index=/teach/database/genome/Ensembl/Homo_sapiens/GRCh38_release95/Homo_sapiens.GRCh38.cdna.all.salmon/
input=/teach/project/Human-16-Asthma-Trans/data/cleandata/trim_galore
outdir=/teach/project/Human-16-Asthma-Trans/Expression/salmon

# 單樣本測試
salmon quant -i $index -l A \
-1 $input/SRR1039510_1_val_1.fq.gz \
-2 $input/SRR1039510_2_val_2.fq.gz \
-p 5 -o $outdir/SRR1039510.quant

# 編寫腳本，使用salmon批量對目錄下所有fastq文件進(jìn)行定量
cat /teach/project/Human-16-Asthma-Trans/data/rawdata/sra/sampleId.txt |while read id 
do
 echo "salmon quant -i ${index} -l A -1 ${input}/${id}_1_val_1.fq.gz -2 ${input}/${id}_2_val_2.fq.gz -p 5 -o ${outdir}/${id}.quant"
done >salmon.sh


# 后臺運行腳本
nohup bash salmon.sh 1>salmon.log 2>&1 &

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