LAPA

从3'-seq、长读长和短读长等不同数据源检测选择性多腺苷酸化。

安装

pip install lapa

从长读长RNA-seq或3'-seq中调用Poly(A)位点

lapa --alignment {rep1.bam},{rep2.bam},{rep3.bam} \
	--fasta {fasta} \
	--annotation {gtf} \
	--chrom_sizes {chrom_sizes} \
	--output_dir {output}

参数详情 (文档)

$ lapa --help

Usage: lapa [OPTIONS]

  CLI interface for lapa polyA cluster calling.

Options:
  --alignment TEXT                Single or multiple bam file paths are
                                  separated with a comma.Alternatively, CSV
                                  file with columns of sample, dataset, path
                                  where the sample columns contains the name
                                  of the sample, the dataset is the group of
                                  samples replicates of each other, and path
                                  is the path of bam file.  [required]
  --fasta TEXT                    Genome reference (GENCODE or ENSEMBL fasta)
                                  [required]
  --annotation TEXT               Standart genome annotation (GENCODE or
                                  ENSEMBL gtf). GENCODE gtf file do not
                                  contains annotation for `five_prime_utr` and
                                  `three_prime_utr` so need to be corrected
                                  with `gencode_utr_fix` (see https://github.c
                                  om/MuhammedHasan/gencode_utr_fix.git).
                                  [required]
  --chrom_sizes TEXT              Chrom sizes files (can be generated with
                                  `faidx fasta -i chromsizes > chrom_sizes`)
                                  [required]
  --output_dir TEXT               Output directory of LAPA. See
                                  lapa.readthedocs.io/en/latest/output.html)
                                  for the details of the directory structure
                                  and file format.  [required]
  ...

建议设置包括所有样本及其生物样本/实验重复（组织、细胞系）

samples.csv

sample,dataset,path
ENCFF772LYG,myoblast,ENCFF772LYG.bam
ENCFF421MIL,myoblast,ENCFF421MIL.bam
ENCFF699KOR,myotube,ENCFF699KOR.bam
ENCFF731HHB,myotube,ENCFF731HHB.bam

然后LAPA以samples_config.csv为输入

lapa --alignment samples.csv \
	--fasta {fasta} \
	--annotation {gtf} \
	--chrom_sizes {chrom_sizes} \
	--output_dir {output}
 ...

从长读长RNA-seq中进行TSS调用

lapa_tss --alignment samples.csv \
	--fasta {fasta} \
	--annotation {gtf} \
	--chrom_sizes {chrom_sizes} \
	--output_dir {output}

参数详情 (文档)

$ lapa_tss --help

Usage: lapa_tss [OPTIONS]

  CLI interface for lapa tss cluster calling.

Options:
  --alignment TEXT                Single or multiple bam file paths are
                                  separated with a comma.Alternatively, CSV
                                  file with columns of sample, dataset, path
                                  where the sample columns contains the name
                                  of the sample, the dataset is the group of
                                  samples replicates of each other, and path
                                  is the path of bam file.  [required]
  --fasta TEXT                    Genome reference (GENCODE or ENSEMBL fasta)
                                  [required]
  --annotation TEXT               Standart genome annotation (GENCODE or
                                  ENSEMBL gtf). GENCODE gtf file do not
                                  contains annotation for `five_prime_utr` and
                                  `three_prime_utr` so need to be corrected
                                  with `gencode_utr_fix` (see https://github.c
                                  om/MuhammedHasan/gencode_utr_fix.git)
                                  [required]
  --chrom_sizes TEXT              Chrom sizes files (can be generated
                                  with)`faidx fasta -i chromsizes >
                                  chrom_sizes`)  [required]
  --output_dir TEXT               Output directory of LAPA. See
                                  lapa.readthedocs.io/en/latest/output.html)
                                  for the details of the directory structure
                                  and file format.  [required]

文档

有关其他功能、LAPA的参数、Python API和统计测试，请参阅以下文档链接

Readthedocs: https://lapa.readthedocs.io/en/latest/index.html

API参考: https://lapa.readthedocs.io/en/latest/autoapi/index.html

Colab教程（肌母细胞肌管细胞分化的分析）：https://colab.research.google.com/drive/1QzMxCRjCk3i5_MuHzjozSRWMaJgdEdSI?usp=sharing

引用

如果您在学术研究中使用LAPA，请引用以下论文

@article{celik2022analysis,
  title={Analysis of alternative polyadenylation from long-read or short-read RNA-seq with LAPA},
  author={Celik, Muhammed Hasan and Mortazavi, Ali},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}