Noteworthy changes in hichipper¶
Split .fastq files as input to HiC-Pro¶
As of version 0.5.3
of hichipper, users should be able to input split .fastq
files into HiC-Pro
and have hichipper function properly. No extra user flags are needed for this functionality. Thanks
to our early users for helping us figure this out.
A note on duplicate PETs in loops¶
In certain versions (0.4.4
to 0.5.3
) of hichipper, duplicates were not being filtered out
by default. These duplicates were potentially inflating the number of PETs mapping to loops only.
In version 0.7.1
, peaks are now called using all reads without again filtering duplicates
as this is done during the HiC-Pro step.