<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><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 id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">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">sujaikumar@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Dashes in transcript predictions<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><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/join.pm. 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 id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Sujai <<a href="mailto:sujaikumar@gmail.com">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">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">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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