User: keith

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keith130
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130
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3 years, 9 months ago
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5 years, 3 months ago
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k****@bradnam.co

Posts by keith

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Comment: C: cegma : output report
... Not directly from CEGMA. You can turn on verbose mode to get extra output from the last step which would give you information to use in a custom script to then go back and extract the sequences. ...
written 4.3 years ago by keith130
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Comment: C: Error While Running Cegma (Geneid-Train Step)
... Your N50 is 607 bp?!? Or did you mean 607 Kbp. If it really is 607 bp then you should probably not be doing anything else with that genome assembly. ...
written 4.3 years ago by keith130
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Answer: A: cegma : output report
... There are two sets of core eukaryotic genes (CEGs), a larger set (458 CEGs) that are designed to be used to help train a gene finder in novel genomes. All of the CEGMA output except the completeness report file refer to this larger set of core genes.  A subset of the 458 CEGs can be used to assess ...
written 4.3 years ago by keith130
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Comment: C: CEGMA report meaning
... There is no good or bad answer to this. The average number of orthologs per predicted CEG might be expected to be much higher in polyploid genomes that have undergone several whole genome duplications. However, it might also be higher due to a genome assembly that has fully resolved heterozygous reg ...
written 4.3 years ago by keith130
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Answer: A: How to cite genome assemblies?
... Citing versions of any particular bioinformatics/genomics resources can get tricky because there is often no formal publication for every release of a given dataset. Further complicating the situation is the fact that you will often come across different dates (and even names) for the same resource. ...
written 4.4 years ago by keith130
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Answer: A: Makeblastdb Error
... I blogged about this problem http://www.acgt.me/blog/2014/5/15/fun-with-an-error-message-from-ncbi-blast I think the point of this message is to warn you that if your sequence is highly enriched for ambiguous characters (X for proteins, N, R, S etc. for DNA) then you probably won't be able to make ...
written 5.3 years ago by keith130
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Comment: C: Trouble running CEGMA on the sample dataset
... Ah so that's where it went! Thanks for letting me know. I guess this merits a small release to the CEGMA code (and I was hoping to not have to touch CEGMA v2 again!). ...
written 5.3 years ago by keith130
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Answer: A: Trouble running CEGMA on the sample dataset
... Hmm, not for the first time an answer I posted to this thread failed to post (or was removed?). 2nd attempt… I think I have an answer. To test it, you'll need to change one line of code in two different Perl module (it's the same line of code). Make backups of geneid.pm and HMMstar.pm (in CEGMA/lib ...
written 5.3 years ago by keith130
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Answer: A: Trouble running CEGMA on the sample dataset
... Hi again,   I think I (finally) might have a fix. The problem might result from people with newer versions of Perl in which an old Perl function is deprecated (in certain situations).   To test whether this is the case, you'll need to change one line in each of the geneid.pm and HMMstar.pm files ...
written 5.3 years ago by keith130
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Answer: A: Trouble running CEGMA on the sample dataset
... Hmm, I'm pretty stumped by this. Not sure why everything would work until that one specific part of the geneid-train script. The only thing I can think of is to really nail down as to which part of the script is causing the problem. My suggestion:   1. Create a copy of the geneid-train script (e.g ...
written 5.3 years ago by keith130

Latest awards to keith

Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Trouble running CEGMA on the sample dataset
Scholar 4.4 years ago, created an answer that has been accepted. For A: Trouble running CEGMA on the sample dataset
Appreciated 5.3 years ago, created a post with more than 5 votes. For A: Trouble running CEGMA on the sample dataset
Scholar 5.3 years ago, created an answer that has been accepted. For A: Trouble running CEGMA on the sample dataset
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Trouble running CEGMA on the sample dataset

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