<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">maker_functional_fasta reads the results of a blast report. It must be a tab delimted blast report (-outfmt 6 under BLAST+) with unpirot as the database and the maker fasta file as the query. If you renamed the transcripts in the fasta before running maker_functional_fasta, the results in the blast report will no longer match (because they have new names). Use the map_data_ids script to fix names in the blast report if you did that.<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""><div class=""><div><blockquote type="cite" class=""><div class="">On Sep 19, 2016, at 2:30 AM, Xabier Vázquez Campos <<a href="mailto:xvazquezc@gmail.com" class="">xvazquezc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class="">Hi Carson,<br class=""><br class=""></div>I'm trying to go through the post processing step in the tutorial (GMOD2014) but I think something is not right with the functional annotation as no new information is added to the *.putative_function.* files when I run the maker_functional_gff or the maker_functional_fasta. All the fasta headings remain unchanged and the gff files don't show any change. I'm using Maker 2.31.6 by the way.<br class=""><br class=""></div><div class="">Because there are no examples showing what I should expect I'm a bit lost.<br class=""><br class=""></div><div class="">These are my files prior to the functional annotation.<br class=""><br class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">FRL.all.iprscan.renamed.tsv<br class="">FRL.all.maker.proteins.blastout.sprot.renamed.tsv<br class="">FRL.all.maker.proteins.renamed.fasta<br class="">FRL.all.maker.transcripts.renamed.fasta<br class="">FRL.all.maker.trnascan.transcripts.renamed.fasta<br class="">FRL.all.renamed.gff<br class="">FRL.map<br class=""></blockquote><br class=""></div><div class="">And this, an example of the command I'm using<br class=""><br class="">maker_functional_fasta uniprot_sprot.fasta FRL.all.maker.proteins.blastout.sprot.renamed.tsv FRL.all.maker.proteins.renamed.fasta > FRL.all.maker.proteins.renamed.putative_function.fasta </div><div class=""><br class=""></div><div class="">Thank you in advance.<br class=""><br class=""></div><div class="">Xabi<br class=""></div><div class=""></div><div class=""><br class=""><br class="">PS: the tutorial mentions to use the "standard" IPRS output but by default it gives xml, gff3 and tsv files. Which one should I use?<br clear="all" class=""></div><div class=""><div class=""><div class=""><br class="">-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">Xabier Vázquez-Campos, <i class="">PhD</i><br class=""><i class="">Research Associate</i><br class="">Water Research Centre<br class="">School of Civil and Environmental Engineering<br class="">
The University of New South Wales<br class="">Sydney NSW 2052 AUSTRALIA<br class=""></div></div></div></div></div></div></div>
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