FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads.

Reference:

• Kruse, Kai, Clemens B. Hug, and Juan M. Vaquerizas. "FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data." Genome biology 21.1 (2020): 1-19.

• FAN-C Main Site
• FAN-C on GitHub

• Module Name: fanc (see the modules page for more information)
• FAN-C is multithreaded. Please use the option argument pair -t $SLURM_CPUS_PER_TASK as shown below.
• This application produces PDF reports. You can use hpcdrive to view these reports on your local workstation.
• Path to example files is set in the FANC_EXAMPLES environment variable after loading the module.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive -c8 --mem=16g --gres=lscratch:30
salloc.exe: Pending job allocation 11754716
salloc.exe: job 11754716 queued and waiting for resources
salloc.exe: job 11754716 has been allocated resources
salloc.exe: Granted job allocation 11754716
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0996 are ready for job
srun: error: x11: no local DISPLAY defined, skipping
error: unable to open file /tmp/slurm-spank-x11.11754716.0
slurmstepd: error: x11: unable to read DISPLAY value

[user@cn0996 ~]$ module load fanc
[+] Loading fanc  0.9.17  on cn0996
[+] Loading singularity  3.7.2  on cn0996

[user@cn0996 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn0996 11754716]$ cp $FANC_EXAMPLES .

[user@cn0996 11754716]$ unzip examples.zip
Archive:  examples.zip
   creating: examples/
  inflating: examples/SRR4271982_chr18_19_2.fastq.gzip
[snip...]
  inflating: examples/SRR4271982_chr18_19_1.fastq.gzip

[user@cn0996 11754716]$ cd examples/

[user@cn0996 examples]$ fanc auto SRR4271982_chr18_19_1.fastq.gzip SRR4271982_chr18_19_2.fastq.gzip \
    output/ -g hg19_chr18_19.fa -i hg19_chr18_19/hg19_chr18_19 -n fanc_example \
    -t ${SLURM_CPUS_PER_TASK} -r HindIII --split-ligation-junction -q 30
2021-03-30 13:07:51,440 INFO FAN-C version: 0.9.17
2021-03-30 13:07:51,443 INFO Output folder: output/
2021-03-30 13:07:51,443 INFO Input files: SRR4271982_chr18_19_1.fastq.gzip, SRR4271982_chr18_19_2.fastq.gzip
2021-03-30 13:07:51,443 INFO Input file types: fastq, fastq
2021-03-30 13:07:51,443 INFO Final basename: fanc_example (you can change this with the -n option!)
[...snip]
2021-03-30 13:22:16,001 INFO Total: 556663. Filtered: 294
Expected 100% (556369 of 556369) |###########################################| Elapsed Time: 0:00:08 Time:  0:00:08
2021-03-30 13:22:29,543 INFO Done.
2021-03-30 13:22:33,641 INFO Saving statistics...
2021-03-30 13:22:33,832 INFO Normalising binned Hic file
Expected 100% (556369 of 556369) |###########################################| Elapsed Time: 0:00:08 Time:  0:00:08
Closing remaining open files:output/hic/fanc_example.hic...done

[user@cn0996 examples]$ fancplot chr18:63mb-70mb -p triangular -vmax 0.05 output/hic/binned/fanc_example_100kb.hic
2021-03-30 13:29:15,888 INFO Found 1 regions
Closing remaining open files:output/hic/binned/fanc_example_100kb.hic...done

[user@cn0996 examples]$ ls -lh
total 558M
drwxr-xr-x 9 user user 4.0K Aug  6  2020 architecture
drwxr-xr-x 2 user user 4.0K Feb  4  2020 bwa-index
drwxr-xr-x 2 user user 4.0K Feb  4  2020 hg19_chr18_19
-rw-r--r-- 1 user user 134M Feb  4  2020 hg19_chr18_19.fa
-rw-r--r-- 1 user user 996K Feb  4  2020 hg19_chr18_19_re_fragments.bed
drwxr-xr-x 2 user user 4.0K Aug  6  2020 hicpro
drwxr-x--- 7 user user 4.0K Mar 30 13:07 output
-rw-r--r-- 1 user user 200M Feb  4  2020 SRR4271982_chr18_19_1.fastq.gzip
-rw-r--r-- 1 user user 200M Feb  4  2020 SRR4271982_chr18_19_2.fastq.gzip
-rw-r--r-- 1 user user  52K Feb  4  2020 test.cool
-rw-r--r-- 1 user user  24M Feb  4  2020 test.hic

[user@cn0996 examples]$ exit
exit
salloc.exe: Relinquishing job allocation 11754716
salloc.exe: Job allocation 11754716 has been revoked.

[user@biowulf ~]$

Create a batch input file (e.g. fanc.sh). For example:

#!/bin/bash
set -e
module load fanc

fanc auto SRR4271982_chr18_19_1.fastq.gzip SRR4271982_chr18_19_2.fastq.gzip \
    output/ -g hg19_chr18_19.fa -i hg19_chr18_19/hg19_chr18_19 -n fanc_example \
    -t ${SLURM_CPUS_PER_TASK} -r HindIII --split-ligation-junction -q 30

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] fanc.sh

Create a swarmfile (e.g. fanc.swarm). For example:

fanc auto a.fastq.gzip chrN.fastq.gzip outa -g N.fa -t $SLURM_CPUS_PER_TASK <opts> 
fanc auto b.fastq.gzip chrN.fastq.gzip outb -g N.fa -t $SLURM_CPUS_PER_TASK <opts> 
fanc auto c.fastq.gzip chrN.fastq.gzip outc -g N.fa -t $SLURM_CPUS_PER_TASK <opts> 
fanc auto c.fastq.gzip chrN.fastq.gzip outd -g N.fa -t $SLURM_CPUS_PER_TASK <opts> 

Submit this job using the swarm command.

swarm -f fanc.swarm [-g #] [-t #] --module fanc