Workflow Type: Galaxy

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

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/0.8.11+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
  • File
HiCUP report (txt) #main/HiCUP report (txt) n/a
  • File
matrix with iced values #main/matrix with iced values n/a
  • File
matrix with raw values #main/matrix with raw values n/a
  • File
plot with pyGenomeTracks #main/plot with pyGenomeTracks n/a
  • File
valid pairs filtered and sorted #main/valid pairs filtered and sorted n/a
  • File
valid pairs in juicebox format #main/valid pairs in juicebox format n/a
  • File
valid pairs in juicebox format MAPQ filtered #main/valid pairs in juicebox format MAPQ filtered n/a
  • File

Version History

v0.3 (latest) Created 16th Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 bd5d233

v0.2.1 Created 2nd Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.2.1


Frozen v0.2.1 c29214f

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
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  • Lucille Delisle
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Created: 21st Jan 2023 at 03:01

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