harvardinformatics / degenotate

harvardinformatics/degenotate Issues

Error GXF1: Invalid number of IDs found during transcript parent id parsing AND Error GXF2: No CDS exons found in input annotation file! Cannot calculate degeneracy without coding sequences
Closed a year ago6
only pN pS calculated, no pvalues or direction
Closed 2 months ago12
How to extract 0-fold and 4-fold sites from VCF files, based on the output of degenotate
Closed 2 months ago3
Extract Conserved 4D sites from alignment
Closed 3 months ago5
ValueError issue
Closed a year ago3
Index out of range
Closed a year ago6
empty bed and .tsv file
Closed a year ago3
**Error SEQ2: Some exons have differing strands
Closed a year ago7
Allow csi index for vcf files
Closed a year ago1
ModuleNotFoundError: No module named 'degenotate_lib'
Closed a year ago10
Degenotate doesn't run, returning KeyError
Closed a year ago14
How to parse GFF/GTF files with their inconsistencies across sources?
Closed 2 years ago6
Mismatch between fasta chromosome names and gff chromosome names
Closed 2 years ago4
Automatically replace ambiguous bases with N
Closed 2 years ago4
Lookup table for codon degeneracy
Closed 2 years ago1
Initial output code
Closed 2 years ago
Test data
Closed 2 years ago2
Reading CDS from individual files
Closed 2 years ago1
Reduce redundant code when reading GXF files
Closed 2 years ago1