使用hisat2+stringtie进行基因预测

比对到转录本，预测基因

cat id1|while read id
do
#hisat2-build 06/${id}.arrow.polish.fasta.masked index/${id}
#hisat2 --dta -p 20 -x index/${id} -1 /public/home/lianglunping/work/HXM/RNA/input/HA798-normal-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/HA798-normal-1A_2.fq.gz -S 08sam/${id}.1.sam
#hisat2 --dta -p 20 -x index/${id} -1 /public/home/lianglunping/work/HXM/RNA/input/HA798-roll-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/HA798-roll-1A_2.fq.gz -S 08sam/${id}.2.sam
#hisat2 --dta -p 20 -x index/${id} -1 /public/home/lianglunping/work/HXM/RNA/input/NPB-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/NPB-1A_2.fq.gz  -S 08sam/${id}.3.sam
#hisat2 --dta -p 20 -x index/${id} -1 /public/home/lianglunping/work/HXM/RNA/input/TR-grass-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/TR-grass-1A_2.fq.gz  -S 08sam/${id}.4.sam
#hisat2 --dta -p 20 -x index/${id} -1 /public/home/lianglunping/work/HXM/RNA/input/TR-normal-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/TR-normal-2A_1.fq.gz  -S 08sam/${id}.5.sam
#samtools view -bS 08sam/$id.1.sam -o 09bam/$id.1.bam
#samtools view -bS 08sam/$id.2.sam -o 09bam/$id.2.bam
#samtools view -bS 08sam/$id.3.sam -o 09bam/$id.3.bam
#samtools view -bS 08sam/$id.4.sam -o 09bam/$id.4.bam
#samtools view -bS 08sam/$id.5.sam -o 09bam/$id.5.bam
#samtools merge -@ 88   $id.merge    09bam/$id.1.bam 09bam/$id.2.bam 09bam/$id.3.bam 09bam/$id.4.bam 09bam/$id.5.bam 
#samtools sort -@ 88 09bam/$id.merge  -o 09bam/$id.s.bam
stringtie -p 10 -o 11sbam/$id.gtf 09bam/$id.s.bam
done

使用TransDecoder将结果整理成evm输入格式

/public/home/fengting/tools/TransDecoder-v5.5.0/util/gtf_genome_to_cdna_fasta.pl H7L1.gtf /public/home/fengting/task/222anno/06/H7L1.arrow.polish.fasta.masked > transcripts.fasta
/public/home/fengting/tools/TransDecoder-v5.5.0/util/gtf_to_alignment_gff3.pl H7L1.gtf > transcripts.gff3
TransDecoder.LongOrfs -t transcripts.fasta
TransDecoder.Predict -t transcripts.fasta
/public/home/fengting/tools/TransDecoder-v5.5.0/util/cdna_alignment_orf_to_genome_orf.pl \
     transcripts.fasta.transdecoder.gff3 \
     transcripts.gff3 \
     transcripts.fasta > transcripts.fasta.transdecoder.genome.gff3

第一步整理后：

hisat2 -p 50 -x masked -1 /public/home/lianglunping/work/HXM/RNA/input/HA798-normal-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/HA798-normal-1A_2.fq.gz | samtools sort -@ 100 > 1.bam
hisat2 -p 50 -x masked -1 /public/home/lianglunping/work/HXM/RNA/input/HA798-roll-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/HA798-roll-1A_2.fq.gz | samtools sort -@ 100 > 2.bam
hisat2 -p 50 -x masked -1 /public/home/lianglunping/work/HXM/RNA/input/NPB-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/NPB-1A_2.fq.gz | samtools sort -@ 100 > 3.bam
hisat2 -p 50 -x masked -1 /public/home/lianglunping/work/HXM/RNA/input/TR-grass-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/TR-grass-1A_2.fq.gz | samtools sort -@ 100 > 4.bam
hisat2 -p 50 -x masked -1 /public/home/lianglunping/work/HXM/RNA/input/TR-normal-1A_1.fq.gz -2 /public/home/lianglunping/work/HXM/RNA/input/TR-normal-2A_1.fq.gz | samtools sort -@ 100 > 5.bam

samtools merge -@ 88   I.merge   1.bam 2.bam 3.bam 4.bam 5.bam 
samtools sort -@ 88 I.merge  -o I.s.bam

stringtie -p 100 -o I.gtf I.s.bam