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.
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.