RNA-seq完整学习手册！

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需耗时两个月！里面网盘资料如果过期了，请直接联系我1227278128，或者我的群201161227，所有的资源都可以在 http://pan.baidu.com/s/1jIvwRD8 此处找到

搜索可以得到非常多的流程，我这里简单分享一些，我以前搜索到的文献。

 

RNA-seq完整学习手册141

北大也有讲RNA-seq的原理

链接：http://pan.baidu.com/s/1kTmWmv9 密码：6yaz

甚至，我还有个华大的培训课程！！！这可是5天的培训教程哦，好像当初还花了五千多块钱的资料！！！

链接：http://pan.baidu.com/s/1nt5OV5B 密码：gyul

RNA-seq完整学习手册294

优酷也有视频，可以自己搜索看看

RNA-seq完整学习手册312

然后还有几个pipeline，就是生信的分析流程，即使你啥都不会，按照pipeline来也不是问题啦

export PATH=/share/software/bin:$PATH

bowtie2-build ./data/GRCh37_chr21.fa  chr21

tophat -p 1 -G ./data/genes.gtf -o P460.thout chr21 ./data/P460_R1.fq  ./data/P460_R2.fq

tophat -p 1 -G ./data/genes.gtf -o C460.thout chr21 ./data/C460_R1.fq  ./data/C460_R2.fq

cufflinks -p 1 -o P460.clout P460.thout/accepted_hits.bam

cufflinks -p 1 -o C460.clout C460.thout/accepted_hits.bam

samtools  view  -h  P460.thout/accepted_hits.bam  >  P460.thout/accepted_hits.sam

samtools  view  -h  C460.thout/accepted_hits.bam  >  C460.thout/accepted_hits.sam

echo ./P460.clout/transcripts.gtf > assemblies.txt

echo ./C460.clout/transcripts.gtf >> assemblies.txt

cuffmerge -p 1 -g ./data/genes.gtf -s ./data/GRCh37_chr21.fa  assemblies.txt

cuffdiff -p 1 -u merged_asm/merged.gtf  -b ./data/GRCh37_chr21.fa  -L P460,C460 -o P460-C460.diffout P460.thout/accepted_hits.bam C460.thout/accepted_hits.bam

samtools  index  P460.thout/accepted_hits.bam

samtools  index  C460.thout/accepted_hits.bam

 

和另外一个

#!/bin/bash

# Approx 75-80m to complete as a script

cd ~/RNA-seq

ls -l data

 

tophat --help

 

head -n 20 data/2cells_1.fastq

 

time tophat --solexa-quals \

-g 2 \

--library-type fr-unstranded \

-j annotation/Danio_rerio.Zv9.66.spliceSites\

-o tophat/ZV9_2cells \

genome/ZV9 \

data/2cells_1.fastq data/2cells_2.fastq                  # 17m30s

 

time tophat --solexa-quals \

-g 2 \

--library-type fr-unstranded \

-j annotation/Danio_rerio.Zv9.66.spliceSites\

-o tophat/ZV9_6h \

genome/ZV9 \

data/6h_1.fastq data/6h_2.fastq                          # 17m30s

 

samtools index tophat/ZV9_2cells/accepted_hits.bam

samtools index tophat/ZV9_6h/accepted_hits.bam

 

cufflinks --help

time cufflinks  -o cufflinks/ZV9_2cells_gff \

-G annotation/Danio_rerio.Zv9.66.gtf \

-b genome/Danio_rerio.Zv9.66.dna.fa \

-u \

--library-type fr-unstranded \

tophat/ZV9_2cells/accepted_hits.bam                  # 2m

 

 

time cufflinks  -o cufflinks/ZV9_6h_gff \

-G annotation/Danio_rerio.Zv9.66.gtf \

-b genome/Danio_rerio.Zv9.66.dna.fa \

-u \

--library-type fr-unstranded \

tophat/ZV9_6h/accepted_hits.bam                      # 2m

 

# guided assembly

time cufflinks  -o cufflinks/ZV9_2cells \

-g annotation/Danio_rerio.Zv9.66.gtf \

-b genome/Danio_rerio.Zv9.66.dna.fa \

-u \

--library-type fr-unstranded \

tophat/ZV9_2cells/accepted_hits.bam                  # 16m

 

 

time cufflinks  -o cufflinks/ZV9_6h \

-g annotation/Danio_rerio.Zv9.66.gtf \

-b genome/Danio_rerio.Zv9.66.dna.fa \

-u \

--library-type fr-unstranded \

tophat/ZV9_6h/accepted_hits.bam                      # 13m

 

 

time cuffdiff -o cuffdiff/ \

-L ZV9_2cells,ZV9_6h \

-T \

-b genome/Danio_rerio.Zv9.66.dna.fa \

-u \

--library-type fr-unstranded \

annotation/Danio_rerio.Zv9.66.gtf \

tophat/ZV9_2cells/accepted_hits.bam \

tophat/ZV9_6h/accepted_hits.bam                        # 7m

 

head -n 20 cuffdiff/gene_exp.diff

 

sort -t$'\t' -g -k 13 cuffdiff/gene_exp.diff \

> cuffdiff/gene_exp_qval.sorted.diff

 

head -n 20 cuffdiff/gene_exp_qval.sorted.diff

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