STRINGTIE安装及使用

参考自

stringtie github

https://github.com/andreaminio/AnnotationPipeline-EVM_based-DClab/blob/master/Pipeline/022_RNAseq_assembly.md

https://github.com/gpertea/gffread

一、安装

cd ~/biosoft
git clone https://github.com/gpertea/stringtie
cd stringtie
make release

二、测试

Test 1: Input consists of only alignments of short reads
stringtie -o short_reads.out.gtf short_reads.bam
Test 2: Input consists of alignments of short reads and superreads
stringtie -o short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
Test 3: Input consists of alignments of long reads
stringtie -L -o long_reads.out.gtf long_reads.bam
Test 4: Input consists of alignments of long reads and reference annotation (guides)
stringtie -L -G human-chr19_P.gff -o long_reads_guided.out.gtf long_reads.bam
Test 5: Input consists of alignments of short reads and alignments of long reads (using --mix option)
stringtie --mix -o mix_reads.out.gtf mix_short.bam mix_long.bam
Test 6: Input consists of alignments of short reads, alignments of long reads and a reference annotation (guides)
stringtie --mix -G mix_guides.gff -o mix_reads_guided.out.gtf mix_short.bam mix_long.bam

三、使用

合并不同组织的多个bam文件

samtools merge -@ 32 /home2/liuxin/Tissues.A.bam A_*.bam

bam2gtf，使用stringtie拼接转录本序列

~/biosoft/stringtie/stringtie Tissues.A.bam -p 16 -v -o Tissues.A.stringtie.gtf -A Tissues.A.stringtie.abundance.txt

根据gtf文件提取转录本序列（gffread安装见官网gffread）

gffread Tissues.A.stringtie.gtf -g ~/reference.fa -w A.transcripts.1.fa

至此，获取得到用于输入到maker的转录本序列。