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:
*.stat
Key summary statistics that show the number of PETs meeting certain criteria*.inter.loop_counts.bedpe
Interchromosomal looping between anchor loci.*.intra.loop_counts.bedpe
Intrachromosomal looping between all anchor loci*.filt.intra.loop_counts.bedpe
Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.*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.*.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.