1.5构建支原体index并比对

blast确定转录组污染为Mycoplasma yeatsii GM274B
1.寻找基因组
https://www.ncbi.nlm.nih.gov/genome/?term=Mycoplasma+yeatsii

查询结果

2.下载基因组和注释

fna和gff

3.转换gff为gtf
使用cufflinks里面gffread

gffread GCF_000875755.1_ASM87575v1_genomic.gff -T -o 274.gtf

4.构建index

./hisat2-build -p 4 -f ../GM274B/274.fna ../GM274B/genome

GTF没有用上...

生成index

5.比对

hisat2 -t -x ../GM274B/genome -1 ../../chem/12h/R19000256LR01-12h_combined_R1.fastq.gz -2 ../../chem/12h/R19000256LR01-12h_combined_R2.fastq.gz -S ../../../lins/aligned/12h274.sam

对比结果

果然36.21%的是支原体=。=

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参考

GTF/GFF文件的差异及其相互转换https://www.jianshu.com/p/48b5a0972301