[maker-devel] Dashes in transcript predictions

[Sujai]

Wow. That was a super quick response. Thanks very much for confirming the
problem and the fixes!


On 24 March 2014 18:15, Carson Holt <carsonhh at gmail.com> wrote:

> 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.
>
> Usage --> perl fix_dash transcript_file.fasta > new_file.fasta
>
> 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.
>
> Thanks,
> Carson
>
> From: Carson Holt <carsonhh at gmail.com>
> Date: Monday, March 24, 2014 at 10:49 AM
> To: Sujai <sujaikumar at gmail.com>, "maker-devel at yandell-lab.org" <
> maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Dashes in transcript predictions
>
> 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.
>
> 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.
>
> Thanks,
> Carson
>
>
> From: Sujai <sujaikumar at gmail.com>
> Date: Monday, March 24, 2014 at 8:15 AM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Dashes in transcript predictions
>
> Dear Maker Team
>
> On a recent run with maker 2.31, I noticed that a couple of the
> transcripts had dashes/hyphens in them.
>
> Example:
> >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
> TTTGATTATTAATTATTTTTGTCTTTATTAA-------AAAATAATTTTGGTACAAACAATCGAATTAATAT-TAATTAAAGTTTTTATCAGCCTTATAAAATCTACGACACCGGCTTTTACCAATGTTTAGCG
> AGTGATTCTCTCAACAGAAGTATCTCCAAATCAATATTCGTTGAATGTAAATGAACCCAAACACCTTATTCTCATTCCTCCGGAAGAAGCTCCTGAATCAACTTTTGATCTCTACAGTAATGTATCTATGAATT
> GCGAAGGAAGAAGTTATTTTCCGAATCAACCAATCATTGTTAATTGGATGTTTAAACATAAAGACTCATATACGACCATAACAAGAGATCACAAAATGGCTACAAGAATAATCACTGCATCAAACAGATCAAAG
> GAAACTAATCTTGATTTGGTCAATATATTTTCTTACCTTACCATAAATGATATCCGCGAAGAAGATGGTGGAGTTTACAAATGTGTGATGACTCAAGGAAGTGTTGACGAAGAACAAGAATTTCTAGTAACTAT
> AAACAATCAAAGTGAAAAGGAAATTGATGTATCCATTTTTTACCAAGATGATGACTTTGTAAGTGTTCGAGCAGCCTTAGAAACAGTCAAGATTTTAGAGAATTACCAGTTTCGATGTTGGTTGTACGACCGGG
> ATAAGACGTATGGTCAAGACGCCGGGAAGCCGACGAAATCGACAGAAAACCGTATAGGTCGTTATTATCAGTCAAAATATTCTGATTGTTCTCAATTTCGCATAGAAAGTTTCTATCAGCTGCCAATTTCTGTT
> AACCGATGGCTGAAAAAAGAACTCAGTTTACAGTCTTTCTTTCAGCCATTTAGCTTTAATTGGGACCCTCAAAAAACCCCTAAAAACAAGAAAATGGTAGTATGGGTTGTTTCTTCCCTACCCTCAGCGGCGAT
> TCGTAATGCAAAGAGAAGAATCAATGAACAATCTTCTCATGTATAA
>
> The protein prediction for this transcript is ok:
>
> >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
>
> MNCEGRSYFPNQPIIVNWMFKHKDSYTTITRDHKMATRIITASNRSKETNLDLVNIFSYLTINDIREEDGGVYKCVMTQGSVDEEQEFLVTINNQSEKEIDVSIFYQDDDFVSVRAALETVKILENYQFRCWLY
>
> DRDKTYGQDAGKPTKSTENRIGRYYQSKYSDCSQFRIESFYQLPISVNRWLKKELSLQSFFQPFSFNWDPQKTPKNKKMVVWVVSSLPSAAIRNAKRRINEQSSHV
>
> Is this a known bug? I tried searching for "dash|hyphen" in the email list
> but couldn't find anything else.
>
> Best wishes,
>
> - Sujai
>
> ps. I pulled out just this one contig and ran maker on it. all the
> .maker.output files are attached.
>
>
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