<div dir="ltr">Wow. That was a super quick response. Thanks very much for confirming the problem and the fixes!<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 24 March 2014 18:15, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>One more note on this. The sequence is actually fully correct if you just remove the '-' characters. So if you don't want to rerun MAKER with the patch, then you can use the attached script to just repair the transcript file by removing the '-' characters. Your GFF3 files and proteins files should already be correct as is.</div>
<div><br></div><div>Usage --> perl fix_dash transcript_file.fasta > new_file.fasta</div><div><br></div><div>You may need to place the script in the .../maker/bin/ directory so it can detect BioPerl if you don't have BioPerl installed system wide.</div>
<div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, March 24, 2014 at 10:49 AM<br>
<span style="font-weight:bold">To: </span> Sujai <<a href="mailto:sujaikumar@gmail.com" target="_blank">sujaikumar@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] Dashes in transcript predictions<br></div><div><div class="h5"><div><br></div><div><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>I've actually never seen that before, but looking through your output it appears to be specifically caused by setting correct_est_fusion=1, and how it interacts with some features of your dataset.</div><div><br>
</div>
<div>I've attached a patch in the form of a file you can use to replace .../maker/lib/maker/<a href="http://join.pm" target="_blank">join.pm</a>. I'm also going to add it to the MAKER download.</div><div><br></div>
<div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Sujai <<a href="mailto:sujaikumar@gmail.com" target="_blank">sujaikumar@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, March 24, 2014 at 8:15 AM<br>
<span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> [maker-devel] Dashes in transcript predictions<br></div><div><br></div><div dir="ltr">Dear Maker Team<br><br>On a recent run with maker 2.31, I noticed that a couple of the transcripts had dashes/hyphens in them.<br>
<br><div>Example:<br>>snap_masked-nGt.0.3.035610-processed-gene-0.2-mRNA-1 transcript offset:261 AED:0.25 eAED:0.25 QI:261|0.4|0.83|0.83|0.8|0.83|6|0|240<br>
TTTGATTATTAATTATTTTTGTCTTTATTAA-------AAAATAATTTTGGTACAAACAATCGAATTAATAT-TAATTAAAGTTTTTATCAGCCTTATAAAATCTACGACACCGGCTTTTACCAATGTTTAGCG AGTGATTCTCTCAACAGAAGTATCTCCAAATCAATATTCGTTGAATGTAAATGAACCCAAACACCTTATTCTCATTCCTCCGGAAGAAGCTCCTGAATCAACTTTTGATCTCTACAGTAATGTATCTATGAATT GCGAAGGAAGAAGTTATTTTCCGAATCAACCAATCATTGTTAATTGGATGTTTAAACATAAAGACTCATATACGACCATAACAAGAGATCACAAAATGGCTACAAGAATAATCACTGCATCAAACAGATCAAAG GAAACTAATCTTGATTTGGTCAATATATTTTCTTACCTTACCATAAATGATATCCGCGAAGAAGATGGTGGAGTTTACAAATGTGTGATGACTCAAGGAAGTGTTGACGAAGAACAAGAATTTCTAGTAACTAT AAACAATCAAAGTGAAAAGGAAATTGATGTATCCATTTTTTACCAAGATGATGACTTTGTAAGTGTTCGAGCAGCCTTAGAAACAGTCAAGATTTTAGAGAATTACCAGTTTCGATGTTGGTTGTACGACCGGG ATAAGACGTATGGTCAAGACGCCGGGAAGCCGACGAAATCGACAGAAAACCGTATAGGTCGTTATTATCAGTCAAAATATTCTGATTGTTCTCAATTTCGCATAGAAAGTTTCTATCAGCTGCCAATTTCTGTT AACCGATGGCTGAAAAAAGAACTCAGTTTACAGTCTTTCTTTCAGCCATTTAGCTTTAATTGGGACCCTCAAAAAACCCCTAAAAACAAGAAAATGGTAGTATGGGTTGTTTCTTCCCTACCCTCAGCGGCGAT TCGTAATGCAAAGAGAAGAATCAATGAACAATCTTCTCATGTATAA<br>
<br>The protein prediction for this transcript is ok:<br><br>>snap_masked-nGt.0.3.035610-processed-gene-0.2-mRNA-1 protein AED:0.25 eAED:0.25 QI:261|0.4|0.83|0.83|0.8|0.83|6|0|240<br>MNCEGRSYFPNQPIIVNWMFKHKDSYTTITRDHKMATRIITASNRSKETNLDLVNIFSYLTINDIREEDGGVYKCVMTQGSVDEEQEFLVTINNQSEKEIDVSIFYQDDDFVSVRAALETVKILENYQFRCWLY<br>
DRDKTYGQDAGKPTKSTENRIGRYYQSKYSDCSQFRIESFYQLPISVNRWLKKELSLQSFFQPFSFNWDPQKTPKNKKMVVWVVSSLPSAAIRNAKRRINEQSSHV<br><div><br></div><div>Is this a known bug? I tried searching for "dash|hyphen" in the email list but couldn't find anything else.</div>
<div><br></div><div>Best wishes,</div><div><br></div><div>- Sujai</div><div><br></div><div>ps. I pulled out just this one contig and ran maker on it. all the .maker.output files are attached.</div><div><br></div><div><br>
</div></div></div>
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