stringtie转录本有参组装

转录组数据：

SRR8002919.0_PE.1.clean.dup.fq.gz SRR8002928.0_PE.1.clean.dup.fq.gz SRR8002944.0_PE.1.clean.dup.fq.gz SRR8002959.0_PE.1.clean.dup.fq.gz SRR8002963.0_PE.1.clean.dup.fq.gz

SRR8002919.0_PE.2.clean.dup.fq.gz  SRR8002928.0_PE.2.clean.dup.fq.gz  SRR8002944.0_PE.2.clean.dup.fq.gz  SRR8002959.0_PE.2.clean.dup.fq.gz  SRR8002963.0_PE.2.clean.dup.fq.gz

SRR8002920.0_PE.1.clean.dup.fq.gz  SRR8002929.0_PE.1.clean.dup.fq.gz  SRR8002945.0_PE.1.clean.dup.fq.gz  SRR8002960.0_PE.1.clean.dup.fq.gz  SRR8002964.0_PE.1.clean.dup.fq.gz

SRR8002920.0_PE.2.clean.dup.fq.gz  SRR8002929.0_PE.2.clean.dup.fq.gz  SRR8002945.0_PE.2.clean.dup.fq.gz  SRR8002960.0_PE.2.clean.dup.fq.gz  SRR8002964.0_PE.2.clean.dup.fq.gz

SRR8002921.0_PE.1.clean.dup.fq.gz  SRR8002942.0_PE.1.clean.dup.fq.gz  SRR8002956.0_PE.1.clean.dup.fq.gz  SRR8002961.0_PE.1.clean.dup.fq.gz  SRR8002965.0_PE.1.clean.dup.fq.gz

SRR8002921.0_PE.2.clean.dup.fq.gz  SRR8002942.0_PE.2.clean.dup.fq.gz  SRR8002956.0_PE.2.clean.dup.fq.gz  SRR8002961.0_PE.2.clean.dup.fq.gz  SRR8002965.0_PE.2.clean.dup.fq.gz

SRR8002926.0_PE.1.clean.dup.fq.gz  SRR8002943.0_PE.1.clean.dup.fq.gz  SRR8002957.0_PE.1.clean.dup.fq.gz  SRR8002962.0_PE.1.clean.dup.fq.gz  SRR8002966.0_PE.1.clean.dup.fq.gz

SRR8002926.0_PE.2.clean.dup.fq.gz  SRR8002943.0_PE.2.clean.dup.fq.gz  SRR8002957.0_PE.2.clean.dup.fq.gz  SRR8002962.0_PE.2.clean.dup.fq.gz  SRR8002966.0_PE.2.clean.dup.fq.gz

基因组数据：

mhl.fa  mhl.gff

1.使用hisat2将转录组数据与基因组比对，得到sam文件

01.hisat2.py 代码如下：

```

import os, sys

#cwd = os.getcwd()

#d=os.chdir("./")

for f in ["SRR8002919.0_PE","SRR8002920.0_PE","SRR8002921.0_PE","SRR8002926.0_PE","SRR8002928.0_PE","SRR8002929.0_PE","SRR8002942.0_PE","SRR8002943.0_PE","SRR8002944.0_PE","SRR8002945.0_PE","SRR8002956.0_PE","SRR8002957.0_PE","SRR8002959.0_PE","SRR8002960.0_PE","SRR8002961.0_PE","SRR8002962.0_PE","SRR8002963.0_PE","SRR8002964.0_PE","SRR8002965.0_PE","SRR8002966.0_PE"]:

    cmd="/home/qiuqiang/zhangyijiuling/software/hisat2-2.1.0/hisat2 -p 8 --dta --no-mixed --no-discordant --summary-file " + f + ".summary.txt -x /home/qiuqiang/qintao/projects/00.genome/mhl.fa \

    -1 /home/qiuqiang/qintao/projects/01.sika_transcriptome/" + f  + ".1.clean.dup.fq.gz \ 

    -2 /home/qiuqiang/qintao/projects/01.sika_transcriptome/" + f  + ".2.clean.dup.fq.gz \ 

    -S " + f + ".sam & "

    print cmd   

    os.system(cmd)

```

2.将sam文件转换为bam，并排序

此处使用Perl脚本 02.convert_sam2bam.pl

```

#!/usr/bin/perl

use strict;

use warnings;

my @sam=<*sam>;

open (O,">$0.sh");

for my $sam(@sam){

    $sam=~/(\S+).sam/;

    my $prefix=$1;

    print O "samtools view -bS $sam | samtools sort > $1.sort.bam\n";

}

close O;

```

得到 02.convert_sam2bam.pl.sh

samtools view -bS SRR8002929.0_PE.sam | samtools sort > SRR8002929.0_PE.sort.bam

samtools view -bS SRR8002945.0_PE.sam | samtools sort > SRR8002945.0_PE.sort.bam

samtools view -bS SRR8002956.0_PE.sam | samtools sort > SRR8002956.0_PE.sort.bam

samtools view -bS SRR8002957.0_PE.sam | samtools sort > SRR8002957.0_PE.sort.bam

samtools view -bS SRR8002959.0_PE.sam | samtools sort > SRR8002959.0_PE.sort.bam

samtools view -bS SRR8002963.0_PE.sam | samtools sort > SRR8002963.0_PE.sort.bam

samtools view -bS SRR8002964.0_PE.sam | samtools sort > SRR8002964.0_PE.sort.bam

samtools view -bS SRR8002965.0_PE.sam | samtools sort > SRR8002965.0_PE.sort.bam

samtools view -bS SRR8002966.0_PE.sam | samtools sort > SRR8002966.0_PE.sort.bam

3.使用stringtie从sort.bam文件中提取gtf文件

03.stringtie.py

```

import os, sys

#cwd = os.getcwd()

#d=os.chdir("./")

for f in ["SRR8002919.0_PE", "SRR8002920.0_PE","SRR8002921.0_PE","SRR8002926.0_PE","SRR8002928.0_PE","SRR8002929.0_PE","SRR8002942.0_PE","SRR8002943.0_PE","SRR8002944.0_PE","SRR8002945.0_PE","SRR8002956.0_PE","SRR8002957.0_PE","SRR8002959.0_PE","SRR8002960.0_PE","SRR8002961.0_PE","SRR8002962.0_PE","SRR8002963.0_PE","SRR8002964.0_PE","SRR8002965.0_PE","SRR8002966.0_PE"]:

    #cmd="stringtie -p 3 -o " + f + ".gtf -l "  + f + " " + f  + ".bam & "

    cmd="stringtie -p 3 -o " + f + "." + f[:-1]+ ".gtf -l "  + f + " " + f + ".sort.bam & "

    print(cmd)   

    os.system(cmd)

```

得到gtf文件：

SRR8002919.0_PE.SRR8002919.0_P.gtf SRR8002928.0_PE.SRR8002928.0_P.gtf SRR8002944.0_PE.SRR8002944.0_P.gtf SRR8002959.0_PE.SRR8002959.0_P.gtf SRR8002963.0_PE.SRR8002963.0_P.gtf SRR8002920.0_PE.SRR8002920.0_P.gtf  SRR8002929.0_PE.SRR8002929.0_P.gtf  SRR8002945.0_PE.SRR8002945.0_P.gtf  SRR8002960.0_PE.SRR8002960.0_P.gtf  SRR8002964.0_PE.SRR8002964.0_P.gtf  SRR8002921.0_PE.SRR8002921.0_P.gtf  SRR8002942.0_PE.SRR8002942.0_P.gtf  SRR8002956.0_PE.SRR8002956.0_P.gtf  SRR8002961.0_PE.SRR8002961.0_P.gtf  SRR8002965.0_PE.SRR8002965.0_P.gtf SRR8002926.0_PE.SRR8002926.0_P.gtf  SRR8002943.0_PE.SRR8002943.0_P.gtf  SRR8002957.0_PE.SRR8002957.0_P.gtf  SRR8002962.0_PE.SRR8002962.0_P.gtf  SRR8002966.0_PE.SRR8002966.0_P.gtf

4.利用gffread文件将gtf转为fa文件

利用04.gtfTOfa.pl

```

#! /usr/bin/perl

use strict;

use warnings;

my @gtf=<*.gtf>;

open (O,">$0.sh");

for my $gtf(@gtf){

print O "gffread -w $gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa $gtf.gtf\n";

}

close O;

```

得到gtfTOfa.pl.sh

gffread -w SRR8002919.0_PE.SRR8002919.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002919.0_PE.SRR8002919.0_P.gtf.gtf

gffread -w SRR8002920.0_PE.SRR8002920.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002920.0_PE.SRR8002920.0_P.gtf.gtf

gffread -w SRR8002921.0_PE.SRR8002921.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002921.0_PE.SRR8002921.0_P.gtf.gtf

gffread -w SRR8002926.0_PE.SRR8002926.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002926.0_PE.SRR8002926.0_P.gtf.gtf

gffread -w SRR8002928.0_PE.SRR8002928.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002928.0_PE.SRR8002928.0_P.gtf.gtf

gffread -w SRR8002929.0_PE.SRR8002929.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002929.0_PE.SRR8002929.0_P.gtf.gtf

gffread -w SRR8002942.0_PE.SRR8002942.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002942.0_PE.SRR8002942.0_P.gtf.gtf

gffread -w SRR8002943.0_PE.SRR8002943.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002943.0_PE.SRR8002943.0_P.gtf.gtf

gffread -w SRR8002944.0_PE.SRR8002944.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002944.0_PE.SRR8002944.0_P.gtf.gtf

gffread -w SRR8002945.0_PE.SRR8002945.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002945.0_PE.SRR8002945.0_P.gtf.gtf

gffread -w SRR8002956.0_PE.SRR8002956.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002956.0_PE.SRR8002956.0_P.gtf.gtf

gffread -w SRR8002957.0_PE.SRR8002957.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002957.0_PE.SRR8002957.0_P.gtf.gtf

gffread -w SRR8002959.0_PE.SRR8002959.0_P.gtf.fa -g /home/qiuqiang/qintao/projects/00.genome/new_ref.fa SRR8002959.0_PE.SRR8002959.0_P.gtf.gtf

最后就得到了fa文件