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
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
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