[maker-devel] query

[Daniel Ence]

Hi Indu, Can you send you some of the error output that maker is printing? Blastx is used at a couple of different steps in maker's pipeline, so it is hard to tell without more information. You might also think about using the swiss prot database as a source for protein sequences.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of indu khatri [indu2287 at gmail.com]
Sent: Wednesday, December 19, 2012 10:33 PM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] query

 Hello Maker-devel
    Thanks for adding me to the list. I am new to this field. I have a query regarding maker annotation.
    I have assembled a fungal Genome with 1590 contigs and was trying to
    annotate it using MAKER pipeline. I only have paired end WGS sequence from
    Illumina HiSeq sequencing which were assembled using CLCbio. I dont have
    any transcriptome data. I am using ESTs of a closer species for validation
    and similarly the protein sequences. I have started annotation but the
    problem is the pipeline gets stuck to the first contig on blastx step and
    doesn't move further. I could not make out the problem. Can you please help
    me out of this.

Thanks and regards

--
<https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8e6a&attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw>Indu Khatri
PhD Research Fellow,
C/o Dr. Srikrishna Subramanian
Institute of Microbial Technology,
Chandigarh-160036,
India

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