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    RNA-seq命令

    生物信息分析
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    • Z
      zhanglu 最后由 编辑

      回复: RNA-seq数据分析
      运行环境：

      docker   run -it -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 /bin/bash

docker   run -it -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /bin/bash

      /opt/hisat2-2.1.0/extract_splice_sites.py /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf > /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/my_index/chrX.ss
/opt/hisat2-2.1.0/extract_exons.py /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf > /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/my_index/chrX.exon

/opt/hisat2-2.1.0/hisat2-build -p 8 --ss /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/my_index/chrX.ss --exon /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/my_index/chrX.exon /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genome/chrX.fa chrX_tran

hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188044_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188044_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188044_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188104_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188104_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188104_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188234_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188234_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188234_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188245_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188245_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188245_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188257_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188257_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188257_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188273_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188273_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188273_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188337_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188337_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188337_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188383_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188383_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188383_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188401_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188401_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188401_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188428_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188428_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188428_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188454_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR188454_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188454_chrX.sam
hisat2 --dta -x /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/indexes/chrX_tran -1 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR204916_chrX_1.fastq.gz -2 /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/samples/ERR204916_chrX_2.fastq.gz -S /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR204916_chrX.sam




samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188044_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188044_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188104_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188104_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188234_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188234_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188245_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188245_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188257_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188257_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188273_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188273_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188337_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188337_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188383_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188383_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188401_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188401_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188428_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188428_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188454_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188454_chrX.sam
samtools sort -@ 8 -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR204916_chrX.bam /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR204916_chrX.sam


/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188044_chrX.bam -l ERR188044 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188044_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188104_chrX.bam -l ERR188104 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188104_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188234_chrX.bam -l ERR188234 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188234_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188245_chrX.bam -l ERR188245 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188245_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188257_chrX.bam -l ERR188257 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188257_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188273_chrX.bam -l ERR188273 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188273_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188337_chrX.bam -l ERR188337 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188337_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188383_chrX.bam -l ERR188383 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188383_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188401_chrX.bam -l ERR188401 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188401_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188428_chrX.bam -l ERR188428 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188428_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188454_chrX.bam -l ERR188454 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR188454_chrX.gtf
/opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR204916_chrX.bam -l ERR204916 -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/ERR204916_chrX.gtf


/opt/stringtie-1.3.3.Linux_x86_64/stringtie --merge -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/genes/chrX.gtf -o /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data/mergelist.txt


gffcompare -r chrX_data/genes/chrX.gtf -G -o merged stringtie_merged.gtf


/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188044/ERR188044_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188044_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188104/ERR188104_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188104_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188234/ERR188234_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188234_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188245/ERR188245_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188245_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188257/ERR188257_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188257_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188273/ERR188273_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188273_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188337/ERR188337_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188337_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188383/ERR188383_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188383_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188401/ERR188401_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188401_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188428/ERR188428_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188428_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR188454/ERR188454_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR188454_chrX.bam
/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/assembly/stringtie_merged.gtf -o ballgown/ERR204916/ERR204916_chrX.gtf /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/map/ERR204916_chrX.bam

python /prepDE.py -i /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu/pub/ballgown
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        anneng 最后由 编辑

        程老师 6个样本

        2. 
/opt/hisat2-2.1.0/extract_splice_sites.py /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf > /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX.ss
/opt/hisat2-2.1.0/extract_exons.py /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf > /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX.exon

/opt/hisat2-2.1.0/hisat2-build -p 8 --ss /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX.ss --exon /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX.exon /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/GCF_000001405.39_GRCh38.p13_genomic.fa chrX_tran



docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H040_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H040_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.sam

docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C029_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C029_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.sam

docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H036_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H036_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.sam

docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C028_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C028_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.sam

docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H009_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H009_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.sam

docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C030_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C030_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.sam


docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.sam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.sam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.sam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.sam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.sam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.sam



docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3


docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.bam -l C028 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/C028.gtf
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.bam -l C029 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/C029.gtf
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.bam -l C030 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/C030.gtf
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.bam -l H009 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/H009.gtf
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.bam -l H036 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/H036.gtf
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.bam -l H040 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/H040.gtf


docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3  

/opt/stringtie-1.3.3.Linux_x86_64/stringtie --merge -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/mergelist.txt


docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3  /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/C028/C028.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.bam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3  /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/C029/C029.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.bam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3  /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/C030/C030.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.bam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3  /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/H009/H009.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.bam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3  /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/H036/H036.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.bam
docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3  


/opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/H040/H040.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.bam


docker   run  -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 


python /prepDE.py -i /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown
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