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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Israel,
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<div>I think that for general annotation purposes, you want to use all of those GFF files during your one make run to annotate the whole genome. If you're interested in exploring which genes are expressed in your different strains and cell stages, then you
can use your annotation results and blast against the different RNA-seq experiments. </div>
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<div>I didn't answer your questions separately, but hopefully that gives some good guidance. If I missed something, let me know.</div>
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<div>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 id="divRpF175838" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> maker-devel-bounces@yandell-lab.org [maker-devel-bounces@yandell-lab.org] on behalf of Israel Barrantes [isradelacon@gmail.com]<br>
<b>Sent:</b> Monday, March 11, 2013 12:34 PM<br>
<b>To:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> [maker-devel] different RNA-seq experiment outputs in separate annotation passes?<br>
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<div>Dear maker-devel,<br>
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I have several RNA-seq experiment outputs that I want to use as input for MAKER annotation:<br>
(1) Illumina 1.3, strain A, cell stage N<br>
(2) Illumina 1.8, strain A, cell stage N<br>
(3) Illumina 1.8, strain B, cell stage N<br>
(4) 454, strain unknown, cell stage M<br>
For each experiment I mapped the reads and produced GTFs with tophat/cufflinks separately (and later converted to GFF3s with the supplied script)<br>
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Q1: Does it make a difference to run a different annotation pass for each GFF3 from tophat/cufflinks?
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Q2: If this is the case, altering the order of passing the cDNA GFFs (e.g., first pass, experiment 1 GFF, then exp.2 in second pass, etc) will produce more or less transcripts?
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Q3: Is it better to simply merge this GFFs into a single nonredundant file (e.g. bedtools intersect) than using them separately, one for each MAKER pass?
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Thank you in advance,<br>
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<div>--<br>
Israel Barrantes<br>
Otto-von-Guericke-Universität<br>
Lehrstuhl für Regulationsbiologie IBIO/FNW<br>
Deutschland<br>
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