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

[ZACHARY STEWART]

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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