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<p class="MsoNormal">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></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'<o:p></o:p></p>
<p class="MsoNormal">>contig_134\<o:p></o:p></p>
<p class="MsoNormal">>contig_149\<o:p></o:p></p>
<p class="MsoNormal">>contig_158\<o:p></o:p></p>
<p class="MsoNormal">>contig_222\<o:p></o:p></p>
<p class="MsoNormal">>contig_316\<o:p></o:p></p>
<p class="MsoNormal">>contig_582\<o:p></o:p></p>
<p class="MsoNormal">>contig_634\<o:p></o:p></p>
<p class="MsoNormal">>contig_700\<o:p></o:p></p>
<p class="MsoNormal">>contig_741\<o:p></o:p></p>
<p class="MsoNormal">…<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chris<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">maker-devel <maker-devel-bounces@yandell-lab.org> on behalf of Carson Holt <carsonhh@gmail.com><br>
<b>Date: </b>Monday, October 16, 2017 at 11:22 AM<br>
<b>To: </b>Emmanuel Nnadi <eennadi@gmail.com><br>
<b>Cc: </b>"maker-devel@yandell-lab.org" <maker-devel@yandell-lab.org><br>
<b>Subject: </b>Re: [maker-devel] Backlash running through my sequence<o:p></o:p></span></p>
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<p class="MsoNormal"><a name="_MailOriginalBody">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></o:p></a></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">—Carson<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <</span><a href="mailto:eennadi@gmail.com"><span style="mso-bookmark:_MailOriginalBody">eennadi@gmail.com</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">>
wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Hi all, <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> I attached the sequence<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Thanks<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><br clear="all">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Nnadi Nnaemeka Emmanuel
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Department of Microbiology,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Faculty of Natural and Applied Science,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Publications: </span><a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank"><span style="mso-bookmark:_MailOriginalBody">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><sample_1.fasta><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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