Paired-end histone ChIP-seq or CUT&RUN

usage: HemTools cut_run_histone [-h] [-j JID] [--short] [--debug] [--broad]
                                [-f INPUT] [-d DESIGN_MATRIX] [--guess_input]
                                [-i INDEX_FILE] [-g GENOME] [-b BLACKLIST]
                                [-s CHROM_SIZE] [-e EFFECTIVEGENOMESIZE]

Named Arguments

-j, --jid

enter a job ID, which is used to make a new directory. Every output will be moved into this folder.

Default: “{{subcmd}}_docs_2024-04-18”

--short

Force to use the short queue. (only if R1+R2 fastq.gz size <=250M)

Default: False

--debug

Not for end-user.

Default: False

--broad

broad peak calling

Default: False

-f, --input

tab delimited 3 columns (tsv file): Read 1 fastq, Read 2 fastq, sample ID

-d, --design_matrix

tab delimited 3 columns (tsv file): treatment sample ID, control sample ID, peakcall ID

--guess_input

Let the program generate the input files for you.

Default: False

Genome Info

-i, --index_file

BWA index file

Default: “/home/docs/checkouts/readthedocs.org/user_builds/hemtools/checkouts/latest/subcmd/../hg19/bwa_16a_index/hg19.fa”

-g, --genome

genome version: hg19, hg38, mm10, mm9.

Default: “hg19”

-b, --Blacklist

Blacklist file

Default: “/home/docs/checkouts/readthedocs.org/user_builds/hemtools/checkouts/latest/subcmd/../hg19/Hg19_Blacklist.bed”

-s, --chrom_size

chrome size

Default: “/home/docs/checkouts/readthedocs.org/user_builds/hemtools/checkouts/latest/subcmd/../hg19/hg19.chrom.sizes”

-e, --effectiveGenomeSize

effectiveGenomeSize for bamCoverage

Default: “2451960000”

Usage

Go to your data directory and type the following.

Step 0: Load python version 2.7.13.

module load python/2.7.13

Step 1: Prepare input files, generate fastq.tsv.

HemTools cut_run_histone --guess_input

    Input fastq files preparation complete! ALL GOOD!
    Please check if you like the computer-generated labels in : fastq.tsv
    Input peakcall file preparation complete! File name: peakcall.tsv

Note

If you are preparing fastq.tsv and peakcall.tsv yourself, please make sure no space anywhere in the file. Note that the seperator is tab. Spaces in file name will cause errors.

Step 2: Check the computer-generated input list (manually), make sure they are correct.

less fastq.tsv

less peakcall.tsv

Note

a random string will be added to the generated files (e.g., fastq.94c049cbff1f.tsv) if they exist before running step 1.

Step 3a: (Narrow Peak) Submit your job.

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

Step 3b: (Broad Peak) Submit your job.

HemTools cut_run_histone -f fastq.tsv -d peakcall.tsv --broad

Tip

If you have both narrow peak histone and broad peak histone data in your fastq.tsv, then the simplest way to run is just run step3a and step3b at the same time (see step3c). Note that HemTools generates data in the current directory, then after everything is finished, move the files to the jid folder. That means, to run step3a and step3b at the same time, you have to create two new folders, see step3c.

Step 3c: Run both narrow peak and broad peak for the same input

mkdir narrowPeak_call
cd narrowPeak_call
ln -s ../*.gz .
ln -s ../*.tsv .
HemTools cut_run_histone -f fastq.tsv -d peakcall.tsv
cd ..

mkdir broadPeak_call
cd broadPeak_call
ln -s ../*.gz .
ln -s ../*.tsv .
HemTools cut_run_histone -f fastq.tsv -d peakcall.tsv --broad

Sample input format

fastq.tsv

This is a tab-seperated-value format file. The 3 columns are: Read 1, Read 2, sample ID.

peakcall.tsv

This is also a tab-seperated-value format file. The 3 columns are: treatment sample ID, control/input sample ID, peakcall ID.

Report bug

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:

HemTools report_bug

Use different genome index

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

Comments

code @ github.