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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">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.
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Thanks,<br>
Daniel <br>
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<div class="PlainText">Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
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<div style="direction: ltr;" id="divRpF111222"><font color="#000000" face="Tahoma" size="2"><b>From:</b> maker-devel-bounces@yandell-lab.org [maker-devel-bounces@yandell-lab.org] on behalf of indu khatri [indu2287@gmail.com]<br>
<b>Sent:</b> Wednesday, December 19, 2012 10:33 PM<br>
<b>To:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> [maker-devel] query<br>
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<div dir="ltr"><span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> Hello Maker-devel</span><br style="font-family:arial,sans-serif; font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> Thanks for adding me to the list. I am new to this field.</span><span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> I have a query regarding maker annotation.</span>
<div><span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> I have assembled a fungal Genome with 1590 contigs and was trying to</span><br style="font-family:arial,sans-serif; font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> annotate it using MAKER pipeline. I only have paired end WGS sequence from</span><br style="font-family:arial,sans-serif; font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> Illumina HiSeq sequencing which were assembled using CLCbio. I dont have</span><br style="font-family:arial,sans-serif; font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> any transcriptome data. I am using ESTs of a closer species for validation</span><br style="font-family:arial,sans-serif; font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> and similarly the protein sequences. I have started annotation but the</span><br style="font-family:arial,sans-serif; font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> problem is the pipeline gets stuck to the first contig on blastx step and</span><br style="font-family:arial,sans-serif; font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> doesn't move further. I could not make out the problem. Can you please help</span><br style="font-family:arial,sans-serif; font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif; font-size:12.800000190734863px"> me out of this.</span>
<div><span style="font-family:arial,sans-serif; font-size:12.800000190734863px"><br>
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<div><span style="font-family:arial,sans-serif; font-size:12.800000190734863px">Thanks and regards</span><br clear="all">
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-- <br>
<a href="https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8e6a&attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw" target="_blank"></a>Indu Khatri<br>
PhD Research Fellow,
<div>C/o Dr. Srikrishna Subramanian<br>
Institute of Microbial Technology,<br>
Chandigarh-160036,<br>
India<br>
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