Difference between revisions of "Thor"
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It has a low traffic google groups page, but a google groups page nonetheless at: | It has a low traffic google groups page, but a google groups page nonetheless at: | ||
| − | * | + | * [https://groups.google.com/forum/#!categories/rgtusers/odinthor https://groups.google.com/forum/#!categories/rgtusers/odinthor] |
| + | |||
| + | == 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. | ||
<ins>Notes</ins>: | <ins>Notes</ins>: | ||
* It follows on the ODIN tool which is largely supersedes. | * It follows on the ODIN tool which is largely supersedes. | ||
Revision as of 15:23, 5 June 2017
Contents
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:
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. 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
