hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler
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Workflow Type: Galaxy
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Tests This workflow take as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file. The pairs are filtered for MAPQ and sorted by cooler to generate a tabix dataset. Cooler is used to generate a balanced cool file to the desired resolution.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Bin size in bp | Bin size in bp | For example 10000 for 10kb |
|
| Interactions to consider to calculate weights in normalization step | Interactions to consider to calculate weights in normalization step | Nothing means genome-wide, '--cis-only' means only Cis interactions, '--trans-only' means only Trans interactions |
|
| No fill-in | No fill-in | Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence |
|
| PE fastq input | PE fastq input | Should be a paired collection with Hi-C fastqs |
|
| Restriction enzyme | Restriction enzyme | Restriction enzyme used e.g. A^GATCT,BglII. Some Hi-C protocols may use several enzymes. To specify several enzymes, use the ':' to separate them e.g. A^GATCT,BglII:A^AGCTT,HindIII:^GATC,DpnII. HiCUP accomodates N in restriction enzyme: e.g. :A^ANCTT |
|
| genome name | genome name | only use genome ids which have bowtie2 indexes |
|
| minimum MAPQ | minimum MAPQ | can be set to 0 for no filtering |
|
| region for matrix plotting | region for matrix plotting | You can use your region of interest or a region known for high level of insulation for example HoxD locus: hg19: chr2:175,689,620-178,604,461 hg38: chr2:174,692,032-177,585,317 mm10: chr2:73,779,626-75,669,724 mm39: |
|
Steps
| ID | Name | Description |
|---|---|---|
| 8 | Hi-C_fastqToPairs_hicup | |
| 9 | Sort pairs and index | toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1 |
| 10 | Hi-C_juicermediumtabixToCool_cooler | |
| 11 | final plot | toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| valid pairs in juicebox format | valid pairs in juicebox format | n/a |
|
| HiCUP report (html) | HiCUP report (html) | n/a |
|
| HiCUP report (txt) | HiCUP report (txt) | n/a |
|
| valid pairs in juicebox format MAPQ filtered | valid pairs in juicebox format MAPQ filtered | n/a |
|
| valid pairs filtered and sorted | valid pairs filtered and sorted | n/a |
|
| matrix with iced values | matrix with iced values | n/a |
|
| matrix with raw values | matrix with raw values | n/a |
|
| plot with pyGenomeTracks | plot with pyGenomeTracks | n/a |
|
Version History
v0.1 (earliest) Created 21st Jan 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.15c0dcf0
Creators and SubmitterLicense
Activity
Views: 1703
Created: 21st Jan 2023 at 03:01
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Teams: iwc, Vertebrate Genomes Pipelines in Galaxy
Organizations: Bots, European Galaxy Team
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Public web page: https://github.com/galaxyproject/iwc
