Comments (3)
ksahlin
commented on August 26, 2024
Hi @unique379r,
uLTRA requires an annotation, and also will not have any advantage over e.g., minimap2 for annotation-free alignment.
I recommend that you use minimap2 or deSALT for annotation-free alignment.
Best,
K
from ultra.
unique379r
commented on August 26, 2024
Hi Again @ksahlin
Thank you for your suggestion but i really wanted to try uLTRA too along with minimap2 and deSALT. Therefore, i got the gtf (https://tinyurl.com/5e8emmf2) but when i tried to make indices, some utility script of uLTRa gives me error. Now sure, why as it seems fine to me, please have a look and looking forward for your help.
uLTRA index chm13v2.0.fasta CHM13.v1.v2.gtf .
ERROR
Traceback (most recent call last):
File "/Apps/envs/ultra/bin/uLTRA", line 714, in <module>
prep_splicing(args, refs_lengths)
File "=Apps/envs/ultra/bin/uLTRA", line 80, in prep_splicing
max_intron_chr, exon_choordinates_to_id, chr_to_id, id_to_chr = augmented_gene.create_graph_from_exon_parts(db, args.flank_size, args.small_exon_threshold, args.min_segm, refs_lengths)
File "=/Apps/envs/ultra/lib/python3.9/site-packages/modules/create_augmented_gene.py", line 323, in create_graph_from_exon_parts
exon_gene_ids = exon.attributes["gene_id"] # is a list of strings
File "/Apps/envs/ultra/lib/python3.9/site-packages/gffutils/attributes.py", line 63, in __getitem__
v = self._d[k]
KeyError: 'gene_id'
My gtf
chr1 Liftoff exon 11136 11635 . - . gene_id "LOFF_G0000001"; transcript_id "LOFF_T0000001"; gene_name "AL627309.3";
chr1 Liftoff exon 11630 11831 . + . gene_id "LOFF_G0000002"; transcript_id "LOFF_T0000002"; gene_name "AP006222.2";
chr1 Liftoff exon 11639 12457 . - . gene_id "LOFF_G0000001"; transcript_id "LOFF_T0000001"; gene_name "AL627309.3";
chr1 Liftoff exon 12900 13433 . + . gene_id "LOFF_G0000002"; transcript_id "LOFF_T0000002"; gene_name "AP006222.2";
chr1 CAT exon 14253 14325 . + . gene_id "CHM13_G0000001"; transcript_id "CHM13_T0000001"; gene_name "CHM13_G0000001";
chr1 CAT exon 14292 14353 . + . gene_id "CHM13_G0000001"; transcript_id "CHM13_T0000002"; gene_name "CHM13_G0000001";
chr1 CAT exon 20566 20905 . + . gene_id "CHM13_G0000001"; transcript_id "CHM13_T0000002"; gene_name "CHM13_G0000001";
chr1 CAT exon 20566 21099 . + . gene_id "CHM13_G0000001"; transcript_id "CHM13_T0000001"; gene_name "CHM13_G0000001";
chr1 Liftoff exon 52976 53422 . - . gene_id "LOFF_G0000003"; transcript_id "LOFF_T0000003"; gene_name "AL731661.1";
chr1 Liftoff exon 53560 53826 . - . gene_id "LOFF_G0000003"; transcript_id "LOFF_T0000003"; gene_name "AL731661.1";
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ksahlin
commented on August 26, 2024
Hi @unique379r,
I tested it on your dataset. Some of the lines in your file have been switched to geneID instead of gene_id. The fields should be consistent as gene_id, so I believe this is a file format error. This can be easily fixed by replacing geneID by gene_id on the lines where it occurs in your GTF file.
The first offending line in the GTF file is pasted below (but there are several lines where this happens)
chrY Gnomon exon 19436164 19436323 . + . geneID "gene-PRYP5"; transcript_id "rna-XM_017030085.2"; gene_name "HSFY1";
Best,
K
from ultra.
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