Comments (5)
suryasaha
commented on August 12, 2024
Does not handle Solyc ids in cases where > 9 genes are added between 2 Solyc ids. Just puts a placeholder for now.
from bio-genomeupdate.
suryasaha
commented on August 12, 2024
Novel genes should have ids starting in the middle of the interval
| Nof genes | Number |
|---|---|
| 1 | 15 |
| 2 | 13,17 |
| 3 | 13,15,17 |
| 4 | 12,14,16,18 |
| 5 | 11,12,14,16,18 |
| 6 | 11,12,13,14,16,18 |
| 7 | 11,12,13,14,15,16,18 |
| 8 | 11,12,13,14,15,16,17,18 |
| 9 | 11,12,13,14,15,16,17,18,19 |
from bio-genomeupdate.
phosmani
commented on August 12, 2024
chromosome 7 issue. Novel gene ID assignment for first genes at the start of chromosome. There are 3 novel genes before old Solyc ID comes up. First one got correct assignment (Alias=Solyc07g004991). But next two genes gives error.
Error:
Parsing GFF3 line 15 of 33349 to count novel genesUse of uninitialized value $prev_mRNA_ITAG24_Solycid in exists at /home/prashant/tools/Bio-GenomeUpdate/scripts/update_maker_names_gff_hard_coded.pl line 113.
Use of uninitialized value $prev_mRNA_ITAG24_Solycid in hash element at /home/prashant/tools/Bio-GenomeUpdate/scripts/update_maker_names_gff_hard_coded.pl line 118.
Parsing GFF3 line 25 of 33349 to count novel genesUse of uninitialized value $prev_mRNA_ITAG24_Solycid in exists at /home/prashant/tools/Bio-GenomeUpdate/scripts/update_maker_names_gff_hard_coded.pl line 113.
Use of uninitialized value $prev_mRNA_ITAG24_Solycid in hash element at /home/prashant/tools/Bio-GenomeUpdate/scripts/update_maker_names_gff_hard_coded.pl line 115.
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suryasaha
commented on August 12, 2024
Using hard coded intervals. Need to automate the namespace distribution
39c2d19
from bio-genomeupdate.
suryasaha
commented on August 12, 2024
from bio-genomeupdate.
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
- Refactor ACE file code out of place_bacs.pl into separate pre-processing script
- 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
- 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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