hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler
Version 1

Workflow Type: Galaxy

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
  • int
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
  • string
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
  • boolean
PE fastq input PE fastq input Should be a paired collection with Hi-C fastqs
  • File[]
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
  • string
genome name genome name only use genome ids which have bowtie2 indexes
  • string
minimum MAPQ minimum MAPQ can be set to 0 for no filtering
  • int
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:
  • string

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
  • File
HiCUP report (html) HiCUP report (html) n/a
  • File
HiCUP report (txt) HiCUP report (txt) n/a
  • File
valid pairs in juicebox format MAPQ filtered valid pairs in juicebox format MAPQ filtered n/a
  • File
valid pairs filtered and sorted valid pairs filtered and sorted n/a
  • File
matrix with iced values matrix with iced values n/a
  • File
matrix with raw values matrix with raw values n/a
  • File
plot with pyGenomeTracks plot with pyGenomeTracks n/a
  • File

Version History

v0.1 (earliest) Created 21st Jan 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 5c0dcf0
help Creators and Submitter
Creator
  • Lucille Delisle
Submitter
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Activity

Views: 32

Created: 21st Jan 2023 at 03:01

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