[maker-devel] Advanced repeat library construction - CRL step 4 assistance

[Xabier Vázquez-Campos]

Hi Zac,
The contig names you indicate shouldn't give any problems. And if you
changed the names of MITE.lib right after creation and before using it
downstream, it shouldn't be an issue.

Have you confirmed if the prior blastx output has any results?

Also, be sure you use the same version of makeblastdb and blastx/blastn. I
remember reading before running the protocol for first time that in some
cases, switching versions could give problems.
And be careful if you copy/paste from the wiki page, there are a few typos
and dashes instead of minus characters in the command line option flags,
all of which will result in errors

Xabi

On 15 October 2017 at 16:02, ZACHARY STEWART <z2.stewart at qut.edu.au> wrote:

> Hello MAKER team,
>
>
> I am hoping I could have a bit of your time if that isn't a problem. I am
> currently performing the advanced repeat library construction as described
> on the MAKER wiki, and everything appears to work as expected until I reach
> "2.1.5 Building examplars". At this point I encounter a problem previously
> documented in the Google group (title: advanced repeat masking library
> constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta"
> and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify
> what you meant by simplifying the sequence names. The genomic contig names
> are in a format such as ">001676F" and I modified the MITE library to
> have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta
> has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]"
> which I have not tried changing since I suspect the name is important for
> later reassociation. If you could point me in the right direction that
> would be very appreciated.
>
>
> Regards,
>
> Zac.
>
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>


-- 
Xabier Vázquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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