# Output¶

## Per-run output files¶

Each time the user runs hichipper, a *.hichipper.log file containing information pertaining to the flow of the software execution is placed in the out directory (specified by the --out flag). Unless otherwise specified, a file ending in hichipper-qcReport.html provides an interactive quality control report for all samples.

## Per-sample output files¶

Per sample, six (yes, 6, but don’t worry– there’s lots of redundancy) output files are created. They are:

1. *.stat Key summary statistics that show the number of PETs meeting certain criteria
2. *.inter.loop_counts.bedpe Interchromosomal looping between anchor loci.
3. *.intra.loop_counts.bedpe Intrachromosomal looping between all anchor loci
4. *.filt.intra.loop_counts.bedpe Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
5. *interactions.all.mango The same set of loops as 4 but with per-loop FDR measures from the loop proximity bias correction algorithm originally implemented in Mango and presented in the same format.
6. *.interaction.txt.gz The same set of loops as 4 but in a compressed format for visualizing with WashU and UCSC Genome Browser tools.

So, outputs 4, 5, and 6 are identical except in presentation. These data are a subset of those presented in 3. Interchromosomal interactions from 2 are often discarded by other preprocessing pipelines, but they may hold value. If the qcReport is generated, then the .stat file won’t tell you anything new. However, if R is not installed on your machine, this will be a useful file for assessing the quality of your library.