使用生成的索引文件对RNA-Seq进行比对拼接
nohup hisat2 -p 8-x /home/czou/lixin/b/chrX_data/indexes/ -1 ERR188044_chrX_1.fastq -2 ERR188044_chrX_2.fastq -S ERR188044.sam &
for i in *1.fastq;
do
i=${i%1.fastq*};
hisat2 -p 8-x /home/czou/lixin/b/chrX_data/indexes/chrX_tran -1 ${i}1.fastq -2 ${i}2.fastq -S ${i}.sam
done
SAM tools 排序及格式转换
samtools sort -@ 8 -o ERR188044_chrX_.bam ERR188044_chrX_.sam
for i in *.sam;
do
i=${i%.sam*};
samtools sort -@ 8 -o ${i}.bam ${i}.sam
done
stringtie 序列初组装
stringtie -p 8 -G /home/czou/lixin/b/chrX_data/genes/chrX.gtf -o ERR188044_chrX_.gtf ERR188044_chrX_.bam
for i in *.bam;
do
i=${i%.bam*};
nohup stringtie -p 8 -G /home/czou/lixin/b/chrX_data/genes/chrX.gtf -o ${i}.gtf ${i}.bam &
done
合并
stringtie --merge -p 8 -G /home/czou/lixin/b/chrX_data/genes/chrX.gtf -o stringtie_merged.gtf /home/czou/lixin/b/chrX_data/mergelist.txt
检测转录本与参考注释的比较
gffcompare -r /home/czou/lixin/b/chrX_data/genes/chrX.gtf -G -o merged stringtie_merged.gtf
评估表达量，并为ballgown包提供输入文件
stringtie -e -B -p 8 -G /home/czou/lixin/b/chrX_data/samples/sam/gtf2/stringtie_merged.gtf -o ballgown/ERR188044_chrX/ERR188044_chrX.gtf /home/czou/lixin/b/chrX_data/samples/fastq/ERR188044_chrX_.bam
for i in *_chrX_.bam;
do
i=${i%_chrX_.bam*}; stringtie -e -B -p 8 -G /home/czou/lixin/b/chrX_data/samples/sam/gtf2/stringtie_merged.gtf -o ballgown/${i}/${i}_chrX.gtf /home/czou/lixin/b/chrX_data/samples/fastq/${i}_chrX_.bam
done
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作者：大新1234
来源：CSDN
原文：https://blog.csdn.net/qq_41933915/article/details/81873596
版权声明：本文为博主原创文章，转载请附上博文链接！
