2. Quick start

2.1 Installation

Create an env.yml file and write the folling contents.

# env.yml
name: nasap_env
dependencies:
- libcurl=7.87.0
- scipy=1.5.2
- pandas=1.1.5
- hvplot=0.7.3
- pip=21.2.2
- bioconda::deeptools=2.5.7
- bioconda::pybigwig=0.3.17
- bioconda::pysam=0.8.3
- bioconda::bioawk=1.0
- bioconda::bedtools=2.30.0
- bioconda::bowtie2=2.3.5.1
- bioconda::fastp=0.22.0
- bioconda::flash=1.2.11
- bioconda::fastq-pair=1.0
- bioconda::samtools=1.13
- pip:
  - nasap==0.2.9

Create and activate conda env.

conda env create -f ./env.yml
conda activate nasap_env

2.2 Download meta and test data

Download the test data here and unzip it.

File directory structure:

test_nasap_data  
|--Homo_sapiens.GRCh38.93.gtf  
|--Homo_sapiens.GRCh38_tf_target.txt  
|--Homo_sapiens.GRCh38_enhancer_target.txt  
|--test_r1.fq.gz  
|--hg38_bowtie2_index  
|--|--hg38_bowtie2_index.1.bt2  
|--|--hg38_bowtie2_index.2.bt2  
|--|--hg38_bowtie2_index.3.bt2  
|--|--hg38_bowtie2_index.4.bt2  
|--|--hg38_bowtie2_index.rev.1.bt2  
|--|--hg38_bowtie2_index.rev.2.bt2  

2.3 Run the test script

nasap all --read1 ./test_nasap_data/test_r1.fq.gz --adapter1 TGGAATTCTCGGGTGCCAAGG --bowtie_index ./test_nasap_data/hg38_bowtie2_index/hg38_bowtie2_index --gtf ./test_nasap_data/Homo_sapiens.GRCh38.93.gtf --output_root ./your_output/ --tf_source ./test_nasap_data/Homo_sapiens.GRCh38_tf_target.txt --cores 4

2.4 Check the output result

Open the index.html file with a browser and view the results.