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Fei Shen edited this page Feb 8, 2023 · 42 revisions

Example 1:

Quick test: in order to demonstrate the functionality of BSATOS, we hereby provide the results (and alignments) of the tool on a smaller dataset (apple ring rot, see in Example 4 below). We used the the aligned reads (BAMs) files of Chromosome 6.

1) BSATOS installation

https://github.com/maypoleflyn/BSATOS/wiki/Installation

2) data download (demo1_chr06)

ftp://bsatos.top/bsatos/demo1_chr06

OR

download the data from baidu: link：https://pan.baidu.com/s/1oEM4Y0dFXTVLvn20eJWOmg password：0lno

  1. BAM file from resistant/susceptible pool (H/L pool), including only chromosome 6

H.bam L.bam

  1. BAM file from parents including only chromosome 6

M.bam P.bam

  1. run BSATOS script to get results using only one-step

bsatos all --o result_folder --r genome.fasta --gtf gene.gtf --pb P.bam --mb M.bam --hb H.bam --lb L.bam

  1. The processing result could be found:

ftp://bsatos.top/bsatos/demo1_chr06/output_files

OR

download the data from baidu: link：https://pan.baidu.com/s/1oEM4Y0dFXTVLvn20eJWOmg password：0lno

Example 2:

Quick test: in order to demonstrate the functionality of BSATOS, we hereby provide the results (and alignments) of the tool on a smaller dataset (apple ring rot, see in Example 4). We used the the aligned reads (BAMs) files of Chromosome 10.

1) BSATOS installation

https://github.com/maypoleflyn/BSATOS/wiki/Installation

2) data download

ftp://bsatos.top/bsatos/demo2_chr10

OR

download from baidu link：https://pan.baidu.com/s/1az1iYtlScyslhLnRlGVK9g?pwd=534s password：534s

  1. BAM file from resistant pool/susceptible (H/L pool), including only chromosome 10 in the input_files: H.bam L.bam

  2. BAM file from parents including only chromosome 10 in the input_files: P.bam M.bam

  3. Download reference genome file and gtf file in the input_files: gene.gtf genome.fasta

3) run BSATOS script to get results using only one-step

bsatos all --o result_folder --r genome.fasta --gtf gene.gtf --pb P.bam --mb M.bam --hb H.bam --lb L.bam

4) the processing result of BSATOS could be found:

ftp://bsatos.top/bsatos/demo2_chr10/output_files

OR

download from baidu link：https://pan.baidu.com/s/1az1iYtlScyslhLnRlGVK9g?pwd=534s password：534s

Examples 3: The examples will take a longer time (~one weeks), if you want to try, please make sure that all the data is downloaded fully.

The application of BSATOS to map key genes associated with apple acidity (Jia et al.2018).

In this study, in a F1 full-sub population of apple cultivar ‘Golden Delicious’ and ‘Jonathan’ extreme progenies with high apple acidity were pooled and sequenced (H_pool); extreme progenies with low apple acidity were pooled and sequenced (L_pool); we try to map the candidate genes and functional mutations associated with apple acidity.

1) BSATOS installation

https://github.com/maypoleflyn/BSATOS/wiki/Installation

2) data download

  1. Paired reads from high/low fruit apple acidity pool

    H pool: SRR7508321

    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR750/001/SRR7508321/SRR7508321_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR750/001/SRR7508321/SRR7508321_2.fastq.gz

    L pool: SRR7508320

    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR750/000/SRR7508320/SRR7508320_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR750/000/SRR7508320/SRR7508320_2.fastq.gz

  2. Paried reads from pollen/maternal parent

    Pollen parent: SRR7510381 Maternal parent: SRR7510382

    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/001/SRR7510381/SRR7510381_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/001/SRR7510381/SRR7510381_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/002/SRR7510382/SRR7510382_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/002/SRR7510382/SRR7510382_2.fastq.gz

  3. Download reference genome file and gtf file

gene.gtf:

ftp://bsatos.top/bsatos/Genome/gene.gtf

genome.fasta:

ftp://bsatos.top/bsatos/Genome/genome.fasta

OR from baidu

link：https://pan.baidu.com/s/1WngQfb1hxio8creUZM-9nA?pwd=mrpp passwd：mrpp

3) run BSATOS script to get results using only one-step

bsatos all --o result_folder --genome genome.fasta --gtf gene.gtf --pf1 P_1.fastq.gz --pf2 P_2.fastq.gz --mf1 M_1.fastq.gz --mf2 M_2.fastq.gz --hf1 H_1.fastq.gz --hf2 H_2.fastq.gz --lf1 L_1.fastq.gz --lf2 L_2.fastq.gz

Example 2: The examples will take a longer time (~one weeks), if you want to try, please make sure that all the data is downloaded fully.

The application of BSATOS to map key genes associated with apple fruit ring rot disease.

In this study, in a F1 full-sub population of apple cultivar ‘Golden Delicious’ and ‘Jonathan’ extreme progenies with resistant phenotype were pooled and sequenced (R_pool); extreme progenies with susceptible phenotype were pooled and sequenced (S_pool); we try to map the candidate genes and functional mutations associated with apple ring rot disease.

1) BSATOS installation

https://github.com/maypoleflyn/BSATOS/wiki/Installation

2) data download

  1. Paired reads from resistant pool (H pool)

    H pool: SRR7510379

    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/009/SRR7510379/SRR7510379_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/009/SRR7510379/SRR7510379_2.fastq.gz

  2. Paired reads from susceptible pool (L pool)

    L pool: SRR7510380

    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/000/SRR7510380/SRR7510380_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/000/SRR7510380/SRR7510380_2.fastq.gz

  3. Paried reads from pollen/maternal parent

Pollen: SRR7510381 Maternal: SRR7510382

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/001/SRR7510381/SRR7510381_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/001/SRR7510381/SRR7510381_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/002/SRR7510382/SRR7510382_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR751/002/SRR7510382/SRR7510382_2.fastq.gz

  1. Download reference genome file and gtf file

ftp://bsatos.top/bsatos/Genome/gene.gtf ftp://bsatos.top/bsatos/Genome/genome.fasta

OR from baidu

link：https://pan.baidu.com/s/1WngQfb1hxio8creUZM-9nA?pwd=mrpp passwd：mrpp

3) run BSATOS script to get results using only one-step

bsatols all --o result_folder --r genome.fasta --gtf gene.gtf --pf1 P_1.fastq.gz --pf2 P_2.fastq.gz --mf1 M_1.fastq.gz --mf2 M_2.fastq.gz --hf1 R_1.fastq.gz --hf2 R_2.fastq.gz --lf1 S_1.fastq.gz --lf2 S_2.fastq.gz

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