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GaoLabXDU / HiSV

HiSV: a computational pipeline for structural variation detection from Hi-C data
MIT License
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The required matrix file should exist in the current folder. running time: 0.00 seconds #3

Open Jasonfengjx opened 1 year ago

Jasonfengjx commented 1 year ago

mycode: HiSV --inter_hic HiSV_test_data/hcc1954/Inter_matrix --intra_hic HiSV_test_data/hcc1954/Intra_matrix --ref test_HiSV/hg19.chrom.sizes --name hcc1954 --cores 20 --output HiSV_test_data/hcc1954/result --cutoff 0.6

GaoLabXDU commented 1 year ago

Hi Jason, There are two possible reasons for this problem.

  1. The number of chromosomes contained in 'hg19.chrom.sizes' file is inconsistent with the number of hi-c matrix files; For example: The example of reference Genome length file: chr9 141213431 chr13 115169878 And the path of input matrix file is as follows: ---Intra_matrix ----K562_50Kb_chr9_chr9.matrix.txt ----K562_50Kb_chr13_chr13.matrix.txt ---Inter_matrix ----K562_50Kb_chr9_chr13.matrix.txt
  2. For the running command you provided, we require that the hic matrix file be named “hcc1954_(binSize//1000)kb_chr_ chr*_matrix.txt“.

I hope my answer can help you. If you have any questions, please let me know.

Thanks, Li