Workflow: THOR - differential peak calling of ChIP-seq signals with replicates
What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
alias | String | Experiment short name/Alias | |
bin_size | Integer (Optional) | Size of underlying bins for creating the signal |
Size of underlying bins for creating the signal |
merge_peaks | Boolean (Optional) | Merge peaks closer than fragment size |
Merge peaks which have a distance less than the estimated mean fragment size (recommended for histone data) |
alias_cond_1 | String (Optional) | Name for condition 1 |
Name to be displayed for condition 1 |
alias_cond_2 | String (Optional) | Name for condition 2 |
Name to be displayed for condition 2 |
pvalue_cutoff | Float (Optional) | P-value cutoff for peak detection |
P-value cutoff for peak detection. Call only peaks with p-value lower than cutoff. [default: 0.1] |
extension_size | Integer[] (Optional) | Comma-separated list of read extension sizes (provide value for every sample) |
Read's extension size for BAM files (comma separated list for each BAM file in config file). If option is not chosen, estimate extension sizes |
annotation_file | File [TSV] | Genome annotation |
Genome annotation file in TSV format |
chrom_length_file | File [Textual format] | Chromosome length file |
Chromosome length file |
remove_duplicates | Boolean (Optional) | Remove the duplicate reads |
Remove the duplicate reads |
bambai_pair_cond_1 | File[] [BAM] | Biological condition 1 |
Coordinate sorted BAM alignment and index BAI files for the first biological condition |
bambai_pair_cond_2 | File[] [BAM] | Biological condition 2 |
Coordinate sorted BAM alignment and index BAI files for the second biological condition |
deadzones_bed_file | File (Optional) [BED] | Dead zones file |
Define blacklisted genomic regions avoided for analysis |
housekeeping_genes_bed_file | File (Optional) [BED] | Housekeeping genes file |
Define housekeeping genes (BED format) used for normalizing |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
thor |
../tools/rgt-thor.cwl
(CommandLineTool)
|
THOR - differential peak calling of ChIP-seq signals with replicates |
Configuration file is autogenerated based on the bambai_pair_cond_1, bambai_pair_cond_2 and chrom_length_file inputs. The following parameters in a configuration file are skipped: genome, inputs1, inputs2. The following arguments are skipped: --report (tool fails to execute) |
sort_bed |
../tools/linux-sort.cwl
(CommandLineTool)
|
Tool sorts data from `unsorted_file` by key |
|
assign_genes |
../tools/iaintersect.cwl
(CommandLineTool)
|
Tool assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic) |
|
bed_to_bigbed |
../tools/ucsc-bedtobigbed.cwl
(CommandLineTool)
|
Tool converts bed file to bigBed |
|
filter_columns |
../tools/custom-bash.cwl
(CommandLineTool)
|
Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename |
|
restore_columns |
../tools/custom-bash.cwl
(CommandLineTool)
|
Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
thor_stderr_log | File [Textual format] | rgt-THOR stderr log |
rgt-THOR stderr log |
cond_1_bigwig_file | File[] [bigWig] | First biological condition ChIP-seq signals |
Postprocessed ChIP-seq signals from the first biological condition samples |
cond_2_bigwig_file | File[] [bigWig] | Second biological condition ChIP-seq signals |
Postprocessed ChIP-seq signals from the second biological condition samples |
diffpeaks_bed_file | File [bigBed] | Estimated differential peaks |
Estimated differential peaks, bigBed |
diffpeaks_annotated_file | File [TSV] | Estimated differential peaks with assigned genes |
File contains nearest gene information for the differential peaks BED file generated by rgt-THOR |
https://w3id.org/cwl/view/git/46a077b51619c6a14f85e0aa5260ae8a04426fab/workflows/rgt-thor.cwl