hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler
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Tests This workflow takes as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file using the middle of the fragment as coordinates. 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 | #main/Bin size in bp | For example 10000 for 10kb |
|
| Interactions to consider to calculate weights in normalization step | #main/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 | #main/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 | #main/PE fastq input | Should be a paired collection with Hi-C fastqs |
|
| Restriction enzyme | #main/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 | #main/genome name | only use genome ids which have bowtie2 indexes |
|
| minimum MAPQ | #main/minimum MAPQ | can be set to 0 for no filtering |
|
| region for matrix plotting | #main/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 | n/a |
| 9 | Sort pairs and index | toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1 |
| 10 | Hi-C_juicermediumtabixToCool_cooler | n/a |
| 11 | final plot | toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| HiCUP report (html) | #main/HiCUP report (html) | n/a |
|
| HiCUP report (txt) | #main/HiCUP report (txt) | n/a |
|
| matrix with iced values | #main/matrix with iced values | n/a |
|
| matrix with raw values | #main/matrix with raw values | n/a |
|
| plot with pyGenomeTracks | #main/plot with pyGenomeTracks | n/a |
|
| valid pairs filtered and sorted | #main/valid pairs filtered and sorted | n/a |
|
| valid pairs in juicebox format | #main/valid pairs in juicebox format | n/a |
|
| valid pairs in juicebox format MAPQ filtered | #main/valid pairs in juicebox format MAPQ filtered | n/a |
|
Version History
v0.1 (earliest) Created 21st Jan 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
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v0.15c0dcf0
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Created: 21st Jan 2023 at 03:01
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