Related Issues (20)
- The order of BACs written to TPF for an assembled BAC contig is reversed HOT 4
- How to handle BACs that are identical within a assembled BAC? Leave one out??? HOT 3
- Handle cases where inserted BAC/BAC contig is flush with either end of WGS
- Change Contig names in TPF line to first or last BAC in the contig in switch points file HOT 2
- BACs and Contigs are inserted in the wrong location for a TPF line after the first insertion HOT 4
- update_coordinates_gff.pl generates error when mapping RF_007 (tomato 150 vcf) to SL2.50 HOT 1
- Remove overlapping BACs/Contig BACs from group_coords output
- Singleton BACs should be inserted in the order of occurence in the filtered group_coords file HOT 1
- Solo BAC end alignments are not handled correctly in get_tpf_sp_tp_with_bacs_inserted_in_sequences_and_gaps HOT 1
- Cannot handle BACs from non-genbank sources
- process_bac_assembly.pl writes BACs to disk in wrong orientation HOT 1
- Some reference and alt alleles are incorrect in vcfs mapped to build 2.50 HOT 2
- Scafold/Contig specific GFF for chr00 Scafold/Contig HOT 1
- ITAG gene naming for novel genes HOT 5
- Assigning Solyc from ITAG2.40 to ITAG2.90 HOT 7
- Update ver # and add fields to attributes column of Maker_ITAG GFF HOT 1
- script to parse SL3.0 chrs using SL2.93 TPF files and extract contigs
- Reimplement fasta parsers with Bioperl
- Use mummer instead of nucmer for dot plots
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