Inputs for hichipperΒΆ
Based on the original design of hichipper
users needed to specify the full HiC-Pro output.
However, in subsequent versions, different inputs are accepted; specifically, only a valid fragments file.
While .bam
files processed via different software (e.g. HiCUP) are not explicitly supported, one
can easily convert .bam
file formats into valid fragment pairs files using a combination of samtools and bedtools
commands, such as this shown below:
samtools sort -n HiCUP_chr22.bam | bamToBed -i - -bedpe |
awk 'OFS="\t" {print $7,$1,int(($2+$3)/2), $9, $4, int(($5+$6)/2), $10}' > sample_converted.allValidPairs
The resulting sample_converted.allValidPairs
file can be used as input to hichipper
, using the --input-vi
flag.