1. Pull a nASAP image from docker hub
docker pull biodancer/nasap:latest
docker run --rm -it -v `pwd`/data:/tmp -w /tmp biodancer/nasap:latest nasap --help
2. Download test data in the link.
3. Unzip the compressed files.
unzip test_nasap_data.zip
The files directory of the folder is as follows.
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
4. Init a docker container with the downloaded data.
cd test_nasap_data && docker run --rm -it -v $(pwd):/home -w /home --name nasap_container biodancer/nasap /bin/bash
5. In docker container, run the script below to assess the test data quality
nasap assessment --read1 ./test_r1.fq.gz --adapter1 TGGAATTCTCGGGTGCCAAGG --bowtie_index ./hg38_bowtie2_index/hg38_bowtie2_index --gtf ./Homo_sapiens.GRCh38.93.gtf --output_root ./test_out
If you want to get more parameters usage, please refer to the python package manual.