Comments (1)
This file should be a tab-separated list of paired chromosome/sequence identifiers (i.e. one pair per line), where each pair specifies two chromosome sequences, from different genome builds, which are homologous. However, this mechanism is now deprecated for calculating structures from hybrid data. Instead it is better to use the latest "master" branch version (not the first release version), which is more advanced.
In the more recent version there should be a chromosome naming file for each genome build (specified with -cn and -cn2 flags); two columns, space/tab separated. These map from the chromosome sequence identifier in the first column (e.g. as appears in the FASTA sequence file) to a simple name, like "chr1", in the second column. For example, for mouse build mm10:
NC_000067.6 chr1
NC_000068.7 chr2
NC_000069.6 chr3
...
The simple name should match another chromosome in the other naming file to define a homologous pair. The "nuc_sequence_names" program is provided to automatically create a naming file; seeking simple chromosome names from the sequence accession codes found in a FASTA file of a genome build. Note that if the sequence names for the genome build are already "chr1", "chr2", "chr3" etc. Then you can use a naming file of the form:
chr1 chr1
chr2 chr2
chr3 chr3
...
And naturally the second column should match the names for the hybrid's other genome build.
from nuc_processing.
Related Issues (11)
- confused with"The number of the ambiguity group to which the paired reads belong" HOT 1
- Getting contact map for individual chromosomes? HOT 1
- Getting genome wide contact map in .npy or related format?
- TypeError when creating restriction enzyme fragment file HOT 1
- Parameter for data without restriction site (e.g. DNase type) HOT 2
- nun for hybrid genome
- No module named 'NucProcess' when running nuc_sequence_names
- Help HOT 1
- How can I solve the OverflowError ? HOT 4
- nuc_tools not included with git clone HOT 1
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