HemTools: a collection of NGS pipelines and bioinformatic analyses

General principles

A typical HemTools command looks like this:

module load python/2.7.13

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

You can always see all available sub-commands by:

HemTools -h
usage: HemTools [-h] [-v]
                {cut_run,chip_seq_pair,chip_seq_single,atac_seq,report_bug,volcano_plot,crispr_seq}
                ...

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,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.
    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

Duplicated reads and unique reads

Duplicated reads refer to reads that have the same 5’end position.

Unique reads refer to uniquely mapped reads as compared to multi-mapped reads.

In all NGS pipelines, we provide results from:

  1. raw reads: .markdup.bam, .all.bw, _peak.NarrowPeak
  2. remove duplicates reads: rmdup.bam, rmdup.bw, rmdup_peak.NarrowPeak
  3. remove duplicates and unique reads: rmdup.uq.bam, rmdup.uq.bw, rmdup.uq_peak.NarrowPeak

For general usage, rmdup.uq is commonly accepted.

For people focusing on HBG1 and HBG2, raw reads or rmdup reads can be used.

Mapping rate is usually > 95% for high quality data.

Duplicated reads could be PCR duplicates or real signals, can be ranging from 5% to 20% for high quality data. I think I’ve seen cases where the duplicate rate is nearly 40% in some GEO datasets.

Multi-mapped reads are not a lot, maybe 1% to 2%. Never seen any data with >10% multi-mapped reads yet.

FAQ

How do I list all of my past analyses?

All the locations of the past analyses are logged here: ~/.hemtools_meta/my_dir.csv

Error loading python

/hpcf/apps/python/install/2.7.13/bin/python: error while loading shared libraries: libpython2.7.so.1.0: cannot open shared object file: No such file or directory

A: Missing python module. Just do module load python

ERROR: temporary directory is not writable: ‘normalize_bw_given_peak_yli11_2021-06-20’

Interesting, this should be an HPC error, not due to HemTools bug.

another test

code @ github.