1、软件安装

单独为leaf cutter创建一个环境 R版本为3.4.1(笔者操作系统为linux red hat,尝试了很多安装版本和方法，唯一可行的是：)

https://github.com/davidaknowles/leafcutter/issues/247

conda create -n r3.4.1 -y -c conda-forge r-base=3.4.1

conda activate r3.4.1

conda install -y -c conda-forge -c bioconda -c davidaknowles r-leafcutter

conda install bioconda::regtools

2、Differential Splicing

Step 0. Alignment

STAR --runThreadN 20 --genomeDir /index/mm10_GRCm38.101_index \
 --readFilesIn $trim/${name}_clean_1P.fq $trim/${name}_clean_2P.fq \
 --outFileNamePrefix $align/${name} --twopassMode Basic --outSAMstrandField intronMotif\
 --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 20 --quantMode TranscriptomeSAM GeneCounts

Step 1. Converting bams to juncs

##官方code
for bamfile in `ls run/geuvadis/*chr1.bam`; do
    echo Converting $bamfile to $bamfile.junc
    samtools index $bamfile
    regtools junctions extract -a 8 -m 50 -M 500000 $bamfile -o $bamfile.junc
    echo $bamfile.junc >> test_juncfiles.txt
done