Sascha Steinbiss
Sascha Steinbiss
Hi, thanks for reporting this. To properly reproduce the error and determine the root cause, though, I need the input sequence you used (`Ps_genome.part-05.fasta`). It would be great if you...
Thanks, I downloaded the file and will try to reproduce the issue. LTRharvest is running quite long... have you masked all short and tandem repeats before running LTRharvest? Otherwise the...
Ouch, I see. Two weeks -- LTRharvest definitely should never run that long! I would strongly advise to at least use RepeatMasker to mask low-complexity repeats in the source. It...
This sound like it could be a corner case depending on feature coordinates. Could you try to isolate the problematic part in your GFF and share it, together with a...
I completely agree (I have been doing something similar separately up to now). So in case of non-joined features (where one feature corresponds to one sequence) the attribute values are...
@yeban The `-retainids` option in `gt extractfeat` should not change the behaviour of `-join`, it would just make sure that the 'original' IDs from the input GFF3 are used to...
@gordon I guess one could implement both approaches and take the parent attribute by default?
No, in fact is hasn't been addressed yet. Looks like interest has faded a bit. Any volunteers? :) I could take a look at how long it would take to...
Correct code file, at least one of them :) I will need to take a closer look myself to give more direction, as I haven't looked at that code for...