1.安装RiboDiff
使用anaconda进行安装,以下两种都可以尝试,
conda create -n ribodiff python=2.7
conda activate ribodiff
conda install -c bioconda ribodiff
conda install -c bioconda/label/cf201901 ribodiff
2.在linux里面生成counts.txt 或者是quant.sf文件
- 用featureCounts生成counts.txt
featureCounts -T 20 -p -a ./gencode.v40.annotation.gtf -o xx.counts.txt xx.bam
或者用salmon生成quant.sf
salmon quant -i ./index/ -l A \
-1 ./xx.fq.gz\
-2 ./xx.fq.gz\
--output xx_quant
3.1 —salmon
在R里面生成合成文件
ibrary(GenomicFeatures)
library(AnnotationDbi)
library(tximport)
library(DESeq2)
library(data.table)
library(tidyverse)
setwd("D:/RNASEQ/quant")
###############################1.counts.txt###################################3
t2s <- fread("t2s_h38_ensembl.txt", data.table = F, header = F); head(t2s)
colnames(g2s) <- c("geneid","symbol")
##找到所有quant.sf文件所在路径 导入salmon文件处理汇总
files <- list.files(pattern="*quant.sf",recursive=T, full.names <