Thor

Introduction

This is one of the newer Differential Peak Callers from Costalab in Aachen.

It has a low traffic google groups page, but a google groups page nonetheless at:

Notes:

• It follows on the ODIN tool which is largely supersedes.
• For normalization it can use the TMM method widelused in RNA-Seq (EdgeR) or a bed-format list of housekeeping genes.

Housekeeping genes

The rationale for this approach is that they are genes that have a stable expression pattern, and so can be used to normalise all the others that don't.

Usage

a first run

The first few runs are usually error-prone. Thor is no exception:

rgt-THOR first.config --report --no-correction --output-dir ./thorfirst -n THOR_DCfirst

Explanation:

• first.config, this is a configuration file, see below
• --output-dir, program will fail to run if this already exists.

The contents of the first.config is as follows:

#rep1
WTIP_S5_L001/WTIP_S5_L001_srtd.bam
WTIP_S5_L002/WTIP_S5_L002_srtd.bam
#rep2
USL1IP_S7_L001/USL1IP_S7_L001_srtd.bam
USL1IP_S7_L002/USL1IP_S7_L002_srtd.bam
#genome
/storage/home/users/as363/w303_genome/w303.fa
#chrom_sizes
/storage/home/users/as363/w303_genome/w303_.sizes
#inputs1
WTINP_S4_L001/WTINP_S4_L001_srtd.bam
WTINP_S4_L002/WTINP_S4_L002_srtd.bam
#inputs2
ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam
ULS1INP_S6_L002/ULS1INP_S6_L002_srtd.bam
   

output from this run

Call DPs on whole genome.
Computing read extension sizes for ChIP-seq profiles
Compute GC-content
[fai_load] build FASTA index.
Compute factors
Normalize input of Signal 0, Rep 0 with factor 0.644
Normalize input of Signal 0, Rep 1 with factor 0.645
Normalize input of Signal 1, Rep 0 with factor 0.647
Normalize input of Signal 1, Rep 1 with factor 0.647
Use global TMM approach 
TMM normalization not successfully performed, do not normalize data
TMM normalization not successfully performed, do not normalize data
TMM normalization not successfully performed, do not normalize data
TMM normalization not successfully performed, do not normalize data
Compute GC-content
Compute factors
Normalize input of Signal 0, Rep 0 with factor 0.644
Normalize input of Signal 0, Rep 1 with factor 0.645
Normalize input of Signal 1, Rep 0 with factor 0.647
Normalize input of Signal 1, Rep 1 with factor 0.647
Use global TMM approach 
Compute HMM's training set
No differential peaks detected