MIPGEN分析smMIP

查看编码：

# 65535是ucs2 1114111是ucs4
python -c "import sys; print sys.maxunicode"

下载python压缩包安装python

mipgen命令：

id=57
script_dir=/home/mxb/Downloads/MIPGEN-master/tools/
threads=8
fqprefix=./${id}
pe_read1=../1.raw_fq/K250002269_L01_${id}_1.fq
pe_read2=../1.raw_fq/K250002269_L01_${id}_2.fq
pear_read1=./${id}_1.indexed.fq
pear_read2=./${id}_2.indexed.fq
mips=/run/media/mxb/harddisk0/data/20230327/MIP/MIP.txt
ext_tag_size=8
lig_tag_size=0
cut_read1=./${id}.assembled.fastq
gref=/home/mxb/MXB/software/test/b37/human_g1k_v37.fasta
bamprefix=./${id}.indexed.sort
python ${script_dir}mipgen_fq_cutter_se.py $pe_read1 -L 15 -o 1 &&
python ${script_dir}mipgen_fq_cutter_se.py $pe_read2 -L 17 -o 2 &&
source /home/mxb/anaconda3/etc/profile.d/conda.sh
conda activate wes
pear -j $threads -f 1.indexed.fq -r 2.indexed.fq -o $fqprefix &&
conda deactivate
python ${script_dir}mipgen_fq_cutter_se.py $cut_read1 -m ${lig_tag_size},${ext_tag_size} -o $fqprefix &&
bwa mem -t $threads -R '@RG\tID:NGS-4\tPL:UNKNOWN\tSM:NGS-2' $gref ${fqprefix}.indexed.fq > ${fqprefix}.indexed.sam &&
samtools view -bS ${fqprefix}.indexed.sam | samtools sort -o $bamprefix &&
samtools view -@ $threads -h $bamprefix |python ${script_dir}mipgen_smmip_collapser.py 8 $bamprefix.collapse -m $mips -f 1 -s -w&&
echo "analysis commands have terminated (successfully or otherwise)"