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Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

Home Page: https://sebastian-gregoricchio.github.io/snHiC/

License: GNU General Public License v3.0

Python 99.06% HTML 0.01% Shell 0.20% R 0.72%
hi-c hic hicexplorer snakemake snakemake-pipeline dchic selfish genova stripenn compartments

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snhic's Issues

error happen when run

snakemake -s $HOME/software/snHiC-main/workflow/snHiC.snakefile --configfile ./snHiC_test/snHiC_test_data_config.yaml --cores 10
Building DAG of jobs...
MissingInputException in line 390 of $HOME/software/snHiC-main/workflow/snHiC.snakefile:
Missing input files for rule D_generate_restriction_file_and_get_chrSizes:
output: temp_resctriction_bed_file.bed, temp_chrSizes_file.txt
affected files:
$HOME/TE/GCF_000003025.6_Sscrofa11.1_genomic.fna.fai

I use the run and get the error ,how to deal with it. thank for your help

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