RunOnBamToBigWig

Takes bam files from Run-On sequencing data as input and writes bigWig files as output to the user-assigned output-dir. Please note that RunOnBamToBigWig does NOT include steps to ensure chrM reads are really from mitochondrial RNA polymerase. All reads mapped to rRNA or chrM will be removed from bigWig files. If you have un-mapped fastq.gz files, please use https://github.com/Danko-Lab/proseq2.0 instead.

Dependencies:

The pipelines depend on several common bioinformatics tools:

• samtools (version: 1.9 http://www.htslib.org/download/)
• bedtools v2.28.0 (http://bedtools.readthedocs.org/en/latest/)
• bedGraphToBigWig (from the Kent source utilities http://hgdownload.cse.ucsc.edu/admin/exe/)

Please make sure you can call the bioinformatics tools from your current working directory.

Citation

Chu, T., Wang, Z., Chou, S. P., & Danko, C. G. (2018). Discovering Transcriptional Regulatory Elements From Run‐On and Sequencing Data Using the Web‐Based dREG Gateway. Current protocols in bioinformatics, e70.

Usage

Takes bam files from Run-On sequencing data as input and writes
bigWig files as output to the user-assigned output-dir.

Requirements in current working directory:
samtools, bedtools, and bedGraphToBigWig.

bash RunOnBamToBigWig.bsh [options]

options:

To get help:
-h, --help             Show this brief help menu.

Required options:
-SE, --SEQ=SE          Bam file from Single-end sequencing.
-PE, --SEQ=PE          Bam file from Paired-end sequencing.
-c, --chrom-info=PATH  Location of the chromInfo table.

I/O options:
-I, --bam=PREFIX.bam   Input bam file. If not specified, will take
                       *.bam in the current working directory as input
-T, --tmp=PATH         Path to a temporary storage directory.
-O, --output-dir=DIR   Specify a directory to store output in.

Required options for SE
-G, --SE_READ=RNA_5prime Single-end sequencing from 5' end of
                         nascent RNA, like GRO-seq.
-P, --SE_READ=RNA_3prime Single-end sequencing from 3' end of
                         nascent RNA, like PRO-seq.

Options for PE
--RNA5=R1_5prime    Specify the location of the 5' end of RNA
                    [default: R1_5prime].
--RNA3=R2_5prime    Specify the location of the 3' end of RNA
                    [default: R2_5prime].
                    Available options: R1_5prime: the 5' end of R1 reads
                                       R2_5prime: the 5' end of R2 reads
-5, --map5=TRUE     Report the 5' end of RNA [default on, --map5=TRUE].
-3, --map5=FALSE    Report the 3' end of RNA,
                    only available for PE [default off, --map5=TRUE].
-s, --opposite-strand=TRUE
                    Enable this option if the RNA are at the different strand
                    as the reads set at RNA5 [default: disable].

Optional operations:
--thread=1         Number of threads can be used [default: 1]

Example:

The pipeline requires chrom info (-c or --chrom-info=PATH). Chrom info is a tab-delimited file with two columns. The first column is the chromosome name and the second is the size of the chromosome. Please see http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes for example

export hg38_chinfo=/local/storage/data/hg38/hg38.chrom.sizes
bash RunOnBamToBigWig.bsh -SE -G -c $hg38_chinfo -I ABC.bam