HemTools Tutorial 4-18-2019¶

Create a test run folder
Installation
Workflow
ATAC-seq example
Single-end ChIP-seq example
Paired-end ChIP-seq example
CUT & RUN example
Report bug
Questionnaire
Comments

Step 0: set up RSA authentication with HPC

Create a test run folder ¶

cd ~

mkdir my_test_run

cd my_test_run

Installation ¶

/research/dept/hem/common/sequencing/chenggrp/pipelines/bin/add_env.sh

Type HemTools -h to see a list of available pipelines.

HemTools: performs NGS pipelines and other common analyses. Contact:
Yichao.Li@stjude.org or Yong.Cheng@stjude.org

positional arguments:
  {cut_run,chip_seq_pair,chip_seq_single,atac_seq,report_bug,rna_seq,my_dir,volcano_plot,crispr_seq}
                        Available APIs in HemTools
    cut_run             CUT & RUN pipeline
    chip_seq_pair       Paired-end ChIP-seq pipeline
    chip_seq_single     Single-end ChIP-seq pipeline
    atac_seq            ATAC-seq pipeline
    report_bug          Email the log files to the developer.
    rna_seq             RNA-seq pipeline
    my_dir              CD, search, and list my dirs
    volcano_plot        Data visualization: Volcano plot
    crispr_seq          Genome-wide CRISPR Screening pipeline

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

Workflow ¶

Note

Since the upgrade from Red Hat 6 to 7, the --short option is not working anymore. Just don’t add this option to your program is OK.

ATAC-seq example ¶

Copy data

mkdir atac_seq

cd atac_seq

ln -s /research/dept/hem/common/sequencing/chenggrp/pipelines/example_data/atac_seq/*.gz .

Run HemTools

module load python/2.7.13

HemTools atac_seq --guess_input

HemTools atac_seq -f fastq.tsv --short

Single-end ChIP-seq example ¶

Copy data

cd ..

mkdir chip_seq_single

cd chip_seq_single

ln -s /research/dept/hem/common/sequencing/chenggrp/pipelines/example_data/chip_seq_single/*.gz .

Run HemTools

module load python/2.7.13

HemTools chip_seq_single --guess_input

HemTools chip_seq_single -f fastq.tsv -d peakcall.tsv --short

Paired-end ChIP-seq example ¶

Copy data

cd ..

mkdir chip_seq_pair

cd chip_seq_pair

ln -s /research/dept/hem/common/sequencing/chenggrp/pipelines/example_data/chip_seq_pair/*.gz .

Run HemTools

module load python/2.7.13

HemTools chip_seq_pair --guess_input

HemTools chip_seq_pair -f fastq.tsv -d peakcall.tsv --short

CUT & RUN example ¶

Copy data

cd ..

mkdir cut_run

cd cut_run

ln -s /research/dept/hem/common/sequencing/chenggrp/pipelines/example_data/cut_run/*.gz .

Run HemTools

module load python/2.7.13

HemTools cut_run --guess_input

HemTools cut_run -f fastq.tsv -d peakcall.tsv --short

Once the job is finished, you will be notified by email with some attachments. If no attachment can be found, it might be caused by an error. In such case, please go to the result directory (where the log_files folder is located) and type:

cd ..

cd atac_seq

cd [YOUR_JOB_ID]

HemTools report_bug

Questionnaire ¶

Please take a minute to complete this HemTools Tutorial questionnaire

Comments ¶

code @ github.