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GPSeq generates growing rings of digestion, as confirmed by super-resolution microscopy (STED). Here, we aim at estimating a genomic region's nuclear 3D position (relative to the nuclear center/lamina) through the combined analysis of sequencing data coming from multiple GPSeq conditions.

Introduction

The GPSeq technique uses a restriction enzyme to cut, with different probability, peripheral and central loci in fixed nuclei. The restricted sites are then ligated to a linker, compatible with both imaging and sequencing.

Imaging is generally used as a validation step, to verify that restriction was properly performed and that growing rings of digestion were generated (confirmed by STED). On the other hand, information on the restricted regions sequence can is obtained through sequencing.

Usually, a GPSeq experiment consists of a series of conditions in which the restriction happens with increasing probability towards the nuclear center. Thus, a non-trivial challenge is to estimate the radial position of a genomic locus or region in a nucleus.

Documentation

Use the sidebar on the right to navigate gpseqc docs!

• Introduction to go back to this page.
• Background contains the mathematical background of the pipeline.
• Installation for how to setup and maintain the pipeline on your local computer.
• Usage subpages for instructions on how to run the scripts included in gpseqc.**
  • Estimate centrality for gpseqc_estimate.
  • Compare ranks for gpseqc_compare.
• Output subpages for details on the scripts output.
  • gpsqec_estimate
  • gpsqec_compare
• Known issues recapitulates previously reported bugs that have not been fixed yet or won't be fixed as not due to gpseqc code itself.
• Contributing on how to contribute to gpseqc.