Hi-C User Pipeline (HiCUP)

[StevenW]

Hi,

I’m a bioinformatician at the Babraham Institute in Cambridge, UK and I’ve just produced a pipeline (named HiCUP) for processing Hi-C sequence data.

The pipeline, comprising several Perl scripts, receives FASTQ data which is then de-multiplexed (if required), mapped against a reference genome and filtered to remove frequently encountered experimental artefacts. The pipeline produces paired read files in SAM/BAM format, each read pair corresponding to a putative Hi-C di-tag.

Although the pipeline should be considered a work-in-progress (we expect to add more functionality and modify various components of the pipeline, such as how HiCUP classifies putative Hi-C artefacts), it has been used successfully by us when analysing Hi-C data.

We would welcome any thoughts you may have on HiCUP, whether they concern its strengths, weaknesses, how it could be improved or future augmentations.

The project’s homepage is: http://www.bioinformatics.babraham.ac.uk/projects/hicup

I look forward to hearing from you and contributing to the Next-Generation Sequencing Community.

Kindest regards,
Steven Wingett

[colindaven]

For those who also didn't know what this is :

"
Hi-C, developed from 3C, identifies long-range genomic interactions. The Hi-C protocol involves formaldehyde-fixing cells to create DNA-protein bonds that cross-link interacting DNA loci. The DNA is then digested and ligated to generate a library of products that were spatially close to each other in the nucleus.
"

[dawe]

Hi,

I’m a bioinformatician at the Babraham Institute in Cambridge, UK and I’ve just produced a pipeline (named HiCUP) for processing Hi-C sequence data.

Whoa! That's pretty interesting. I'm at Brabaham for EagleGenomics Symposium today... do you think we can meet and chat about it?

d

[StevenW]

Hi,

I am based in the Forum. Today is fine to discuss (morning is better).

S