短序列文库多snp位点分析

作者: njmujjc | 来源:发表于2019-01-02 11:21 被阅读0次

trimmomatic PE bis-SP2_L1_1.fq bis-SP2_L1_2.fq trim_SP2_1_paired.fastq trim_SP2_1_unpaired.fastq trim_SP2_2_paired.fastq trim_SP2_2_unpaired.fastqLEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

./stampy.py -g oct4 -h oct4 -t 10 -M '/media/pc/6a524d78-97d1-481c-b068-8116a4d007f8/jjc/zhysnp/诺禾致源测序结果/DDP03479/trim_SPx_1_paired.fastq','/media/pc/6a524d78-97d1-481c-b068-8116a4d007f8/jjc/zhysnp/诺禾致源测序结果/DDP03479/trim_SPx_2_paired.fastq' -o SPx.sam

for ((x=1;x<=51;x++)); do samtools sort -o SP$x.bam SP$x.sam; done

for ((x=1;x<=51;x++)); do samtools index SP$x.bam; done

pysamstats --type variation --fasta '/media/pc/6a524d78-97d1-481c-b068-8116a4d007f8/jjc/zhysnp/oct4-bis.fa' '/home/pc/biosoft/短序列文库snp分析/stampy-1.0.32/SP1.bam' > SP1.txt