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I had issues recently analysing some verkko assemblies (by default this software gives 14 character headings).
ltr_retriever (3.0.1) seemed to be attempting to alter the header IDs (in the .mod file) and went on to report no LTRs in data despite providing both -inharvest and -infinder inputs. moreover multiple candidates were found when analysing different assemblies built using the same data and when I reduced the headers (changing the prefix 'contig_' to 'ctg') the issue seemed to be fixed and multiple candidate were identified.
I believe something is going wrong with ltr_retriever failing to match modified sequence names somewhere. but is there actually a reason to have a 13 character limit? I couldn't see an obvious reason for this and it feels somewhat arbitrary. I understand maybe taking the first word in a space delimited header to remove additional info that is sometimes included for contigs. but in light of the above issues perhaps the limit could be removed/modified accordingly?
The text was updated successfully, but these errors were encountered:
hi,
I had issues recently analysing some verkko assemblies (by default this software gives 14 character headings).
ltr_retriever (3.0.1) seemed to be attempting to alter the header IDs (in the .mod file) and went on to report no LTRs in data despite providing both -inharvest and -infinder inputs. moreover multiple candidates were found when analysing different assemblies built using the same data and when I reduced the headers (changing the prefix 'contig_' to 'ctg') the issue seemed to be fixed and multiple candidate were identified.
I believe something is going wrong with ltr_retriever failing to match modified sequence names somewhere. but is there actually a reason to have a 13 character limit? I couldn't see an obvious reason for this and it feels somewhat arbitrary. I understand maybe taking the first word in a space delimited header to remove additional info that is sometimes included for contigs. but in light of the above issues perhaps the limit could be removed/modified accordingly?
The text was updated successfully, but these errors were encountered: