构建混合物种参考基因组

• 遇到问题，鼠和人的参考基因组，染色体序列名称一样，需要进行区分，不然和gtf对应时有问题

• 给（fastq,gtf）染色体名前面加上物种名区分

## genome ====
less GRCh38.primary_assembly.genome.fa |grep '>' | head
less GRCm39.primary_assembly.genome.fa |grep '>'| head


sed 's/>/>hg38_/g' GRCh38.primary_assembly.genome.fa  > GRCh38_GRCm39_pri_assemby.fa
sed 's/>/>mm10_/g' GRCm39.primary_assembly.genome.fa   >> GRCh38_GRCm39_pri_assemby.fa

less GRCh38_GRCm39_pri_assemby.fa |grep '>' |  head
less GRCh38_GRCm39_pri_assemby.fa |grep '>' |  tail


## gtf ====
gtf_mm10=gencode.vM34.primary_assembly.annotation.gtf
gtf_hg38=gencode.v45.primary_assembly.annotation.gtf
out_gtf=MIX_gencode.vM34_v45_pri.annotation.gtf


cat $gtf_hg38 | grep  '^##' > $out_gtf
cat $gtf_mm10 | grep  '^##' >> $out_gtf

cat $gtf_hg38 | 
grep -v '^##' |
awk -F $'\t' 'BEGIN {OFS = FS} {$1=("hg38_" $1); print}' \
>> $out_gtf

cat $gtf_mm10 | 
grep -v '^##' |
awk -F $'\t' 'BEGIN {OFS = FS} {$1=("mm10_" $1); print}' \
>> $out_gtf



cat GRCh38_GRCm39_pri_assemby.fa | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' > mix_genome_length.txt

RAM ;STAR Manual arg