转录组 fastq to counts

hisat2+stringtie 转录组

###filter
trimmomatic PE -phred33 SRR1951884.sra_1.fastq.gz SRR1951884.sra_2.fastq.gz SRR1951884_1.fq.gz SRR1951884_1_unpaired.fq.gz SRR1951884_2.fq.gz SRR1951884_unpaired.fq.gz ILLUMINACLIP:TruSeq3 -PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
rm SRR1951884_1_unpaired.fq.gz SRR1951884_unpaired.fq.gz
###map
hisat2 -x /vol3/agis/chengshifeng_group/shiyan/05-pea_RNA_seq/00-ref_genome/Pisum_sativum_v1a -1 SRR1951884_1.fq.gz -2 SRR1951884_1.fq.gz -S SRR1951884.sam -p 8
samtools view -bS SRR1951884.sam | samtools sort -@ 8 -o SRR1951884.sorted.bam
rm SRR1951884.sam
###to gtf
stringtie SRR1951884.sorted.bam -e -p 8 -G /vol3/agis/chengshifeng_group/shiyan/03-pea_WGS/pea_ref/Pisum_sativum_v1a_genes.gff3 -o SRR1951884.gtf -l SRR1951884
ls | \grep "SRR1951884" | sort -V | uniq | awk 'BEGIN{OFS="/"} {print $1,$1".gtf"}' > Sample_gtf.txt
###merge gtf
stringtie --merge -p 8 -G /vol3/agis/chengshifeng_group/shiyan/03-pea_WGS/pea_ref/Pisum_sativum_v1a_genes.gff3 -o merged.gtf Sample_gtf.txt
###step2 to V2 gtf
stringtie –e –B -p 8 -G merged.gtf -o SRR1951884.gtf SRR1951884.sorted.bam
stringtie SRR1951884.sorted.bam -e -B -p 8 -G merged.gtf -o SRR1951884_step2.gtf
### to counts number
prepDE.py -i sample_lst.txt