Sequencing-depth and fragment-length normalized bigwiggle track

usage: normalize_bw.py [-h] [-j JID] [-f BAM_LIST] [-g GENOME]
                       [-s GENOME_CHROM_SIZE]

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        normalize_bw_yli11_2019-08-12)
  -f BAM_LIST, --bam_list BAM_LIST
                        tsv 2 columns, output_filename & input bam file(s).
                        Note that multiple bam files can be merged, if
                        multiple files are given, they should be separated by
                        space (default: None)

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, hg38, mm9, mm10. By default,
                        specifying a genome version will automatically update
                        chrom size. (default: hg19)
  -s GENOME_CHROM_SIZE, --genome_chrom_size GENOME_CHROM_SIZE
                        chrome size (default: /home/yli11/Data/Human/hg19/anno
                        tations/hg19.chrom.sizes)

Summary

Generate sequencing-depth normalized (wrt. 1e7) and fragment-length normalized (wrt. 100bp) bigwiggle tracks given a list of bam files using Homer. By default, all reads in your bam files are used.

Ref: http://homer.ucsd.edu/homer/ngs/ucsc.html

Input

A 2-column tsv file. First column is output file name, Second column is bam file(s) with absolute path or without. Note that multiple bam files can be merged. If multiple bam files are given, they should be separated by space in the second column (see below line 1).

output_filename GATA1_S10.markdup.bam GATA1_S9.markdup.bam
Banana  GATA1_S6.markdup.bam
ABC     GATA1_S11.markdup.bam

Usage

hpcf_interactive

module load python/2.7.13

normalize_bw.py -f bam.list

Output

Once finished, you will be notified by email. All generated bw files are located in the job ID folder.

code @ github.