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Those look suspiciously like the remnants of end-of-line control characters. Since Windows, Mac OS X and Linux all use slightly different control characters to mark end-of-line I’d look at the upstream path of where your files come from and how they’ve been
processed by you or others upstream MAKER (were they generated or processed on a MS or Mac server). One bizarre example we’ve seen is that files that simply pass through an MS Outlook server as an e-mail attachment have had their end-of-line characters converted
to MS format. Good luck…
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<div class="">Barry</div>
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<div class="">On Oct 17, 2017, at 1:11 PM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" class="">cjfields@illinois.edu</a>> wrote:</div>
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I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them. Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers
at the end of the line:<o:p class=""></o:p></div>
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cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'<o:p class=""></o:p></div>
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>contig_134\<o:p class=""></o:p></div>
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>contig_149\<o:p class=""></o:p></div>
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>contig_158\<o:p class=""></o:p></div>
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>contig_222\<o:p class=""></o:p></div>
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>contig_316\<o:p class=""></o:p></div>
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>contig_582\<o:p class=""></o:p></div>
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>contig_634\<o:p class=""></o:p></div>
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>contig_700\<o:p class=""></o:p></div>
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>contig_741\<o:p class=""></o:p></div>
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…<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I’m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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chris<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" class="">maker-devel-bounces@yandell-lab.org</a>>
on behalf of Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>><br class="">
<b class="">Date:<span class="Apple-converted-space"> </span></b>Monday, October 16, 2017 at 11:22 AM<br class="">
<b class="">To:<span class="Apple-converted-space"> </span></b>Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>><br class="">
<b class="">Cc:<span class="Apple-converted-space"> </span></b>"<a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a>><br class="">
<b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [maker-devel] Backlash running through my sequence<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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<a name="_MailOriginalBody" class="">I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.<o:p class=""></o:p></a></div>
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<span class="">—Carson<o:p class=""></o:p></span></div>
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<span class=""><o:p class=""> </o:p></span></div>
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<span class=""><o:p class=""> </o:p></span></div>
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<span class=""><o:p class=""> </o:p></span></div>
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<span class="">On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <</span><a href="mailto:eennadi@gmail.com" style="color: purple; text-decoration: underline;" class=""><span class="">eennadi@gmail.com</span><span class=""></span></a><span class="">> wrote:<o:p class=""></o:p></span></div>
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<span class="">Hi all,<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span class="">I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them<o:p class=""></o:p></span></div>
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<span class=""> I attached the sequence<o:p class=""></o:p></span></div>
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<span class="">Thanks<o:p class=""></o:p></span></div>
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<span class=""><o:p class=""> </o:p></span></div>
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<o:p class=""></o:p></span></div>
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<span class="">Nnadi Nnaemeka Emmanuel<o:p class=""></o:p></span></div>
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<span class="">Department of Microbiology,<o:p class=""></o:p></span></div>
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<span class="">Faculty of Natural and Applied Science,<o:p class=""></o:p></span></div>
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<span class="">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p class=""></o:p></span></div>
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<span class="">Publications: </span><a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" style="color: purple; text-decoration: underline;" class=""><span class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</span><span class=""></span></a><span class=""><o:p class=""></o:p></span></div>
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<span class=""><sample_1.fasta><o:p class=""></o:p></span></div>
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<span class=""><o:p class=""> </o:p></span></div>
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