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For the repeats I followed the following protocol:. For this they provide perl scripts. I came up to point 2.

In the one file, they want to have the upstream or downstream 50bp flanking sequences of LTRs having gaps. However, I do not get this file.

Has anybody encountered this problem before? Hello there, Thege understand this is an old thread, but i was wondering if you managed to solve this problem?

I face the same problem with a list of error and no flanking sequence file. LTR-Harvest false positives Maker repeat library construction.

Please log in to add an answer. I have a multi-fasta file containing sequences with headers such as: I'm having trouble changing a gff file.

I think the best way to do this may be the linux command I'm still struggling on maker. What I want to do, is to follow step by step the m I'm trying to annotate genome using Maker.

So far, I have the gene predictions using genemar I have a database of consensus transposon sequences for a model organi Hi, I lrr working on annotation lut long terminal repeats found in plant retrotransposons.

I'm aiming to fully assemble and annotate the D. I have an annotation produced using maker with RNA-seq evidence but many gene models start with T I plan to do comparison analysis on repeat elements among Hello out there looking for ltr rodents.

I would like to use it to I have installed all Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Powered by Biostar version 2.