Advanced repeat library construction - CRL step 4 assistance

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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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Re: 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 <[hidden email]> 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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