<div dir="ltr">would it be possible to get digest mode set up properly?<div>I have it selected but I get emails for each individual message.</div><div><br><div>Thanks</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 13, 2016 at 10:27 AM,  <span dir="ltr"><<a href="mailto:maker-devel-request@yandell-lab.org" target="_blank">maker-devel-request@yandell-lab.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send maker-devel mailing list submissions to<br>
        <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
        <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" rel="noreferrer" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br>
<br>
or, via email, send a message with subject or body 'help' to<br>
        <a href="mailto:maker-devel-request@yandell-lab.org">maker-devel-request@yandell-lab.org</a><br>
<br>
You can reach the person managing the list at<br>
        <a href="mailto:maker-devel-owner@yandell-lab.org">maker-devel-owner@yandell-lab.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of maker-devel digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
   1. Re: Reformat maker gff3 (Michael Campbell)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 13 May 2016 11:34:00 -0400<br>
From: Michael Campbell <<a href="mailto:michael.s.campbell1@gmail.com">michael.s.campbell1@gmail.com</a>><br>
To: Xabier V?zquez Campos <<a href="mailto:xvazquezc@gmail.com">xvazquezc@gmail.com</a>><br>
Cc: Jenny Lee <<a href="mailto:h.lee12@uq.edu.au">h.lee12@uq.edu.au</a>>,      "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>"<br>
        <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
Subject: Re: [maker-devel] Reformat maker gff3<br>
Message-ID: <<a href="mailto:777D8DFF-CB99-4F03-A4CF-8E52F0E4526A@gmail.com">777D8DFF-CB99-4F03-A4CF-8E52F0E4526A@gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
I?ve attached a protocols paper that walks through what you are trying to do. Let me know if it helps.<br>
Mike<br>
<br>
> On May 12, 2016, at 8:37 PM, Xabier V?zquez Campos <<a href="mailto:xvazquezc@gmail.com">xvazquezc@gmail.com</a>> wrote:<br>
><br>
> Can't you filter the file content with the 'grep' command? If you need to extract columns, use 'cut' too<br>
><br>
> On 13 April 2016 at 13:05, Jenny Lee <<a href="mailto:h.lee12@uq.edu.au">h.lee12@uq.edu.au</a> <mailto:<a href="mailto:h.lee12@uq.edu.au">h.lee12@uq.edu.au</a>>> wrote:<br>
> Hi all,<br>
><br>
> I would like to update my maker gff3 file to only contain the genes I've decided to keep - all maker genes, a subset of abinitio genes (which have interproscan hits). I would like to also exclude the repeats information and only retain the CDS, gene, exon and mRNA - like the format we usually see in published data.<br>
><br>
> I've been trying to do this manually and it gets messy. Any ideas?<br>
><br>
> Thanks a lot.<br>
><br>
> Regards,<br>
> Jenny Lee<br>
><br>
><br>
> _______________________________________________<br>
> maker-devel mailing list<br>
> <a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a> <mailto:<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>><br>
> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" rel="noreferrer" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a> <<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" rel="noreferrer" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>><br>
><br>
><br>
><br>
><br>
> --<br>
> Xabier V?zquez-Campos, PhD<br>
> Research Associate<br>
> Water Research Centre<br>
> School of Civil and Environmental Engineering<br>
> The University of New South Wales<br>
> Sydney NSW 2052 AUSTRALIA<br>
> _______________________________________________<br>
> maker-devel mailing list<br>
> <a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>
> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" rel="noreferrer" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20160513/f0f3e46b/attachment.html" rel="noreferrer" target="_blank">http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20160513/f0f3e46b/attachment.html</a>><br>
-------------- next part --------------<br>
A non-text attachment was scrubbed...<br>
Name: bi0411 (1).pdf<br>
Type: application/pdf<br>
Size: 484328 bytes<br>
Desc: not available<br>
URL: <<a href="http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20160513/f0f3e46b/attachment.pdf" rel="noreferrer" target="_blank">http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20160513/f0f3e46b/attachment.pdf</a>><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20160513/f0f3e46b/attachment-0001.html" rel="noreferrer" target="_blank">http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20160513/f0f3e46b/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" rel="noreferrer" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br>
<br>
<br>
------------------------------<br>
<br>
End of maker-devel Digest, Vol 96, Issue 10<br>
*******************************************<br>
</blockquote></div><br></div>