User: maxwhjohn1988

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Posts by maxwhjohn1988

<prev • 24 results • page 1 of 3 • next >
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Comment: C: GAWN - Genome Annotation Without Nightmares
... I would also really like to know the answer to this question. I'm embarking on some annotation for the first time and have no transcriptome from my species of interest (or any congener) so I was hoping to hedge my best by supplying > 1 transcriptome to whichever pipeline I end up using. ...
written 5 weeks ago by maxwhjohn198840
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Comment: C: Running MAKER2 pipeline with Augustus for the first time -- need some guidance
... Hi voidnyx - I'm in a similar position to what you describe here (except that I have no RNAseq / transcriptome data for my species). I've made a post here asking for help but not got any detailed responses. Did you get anywhere with this project? Do you have any advice for someone doing this for ...
written 6 weeks ago by maxwhjohn198840
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Comment: C: Eukaryotic Genome Annotation - Without ESTs or Transcriptomic or Proteomic Data
... Thanks for the reply, ashish. The species is an ant, and it is not in the list unfortunately (it's not a well-studied organism and only a few groups in the world work with it). I've spent all day getting MAKER installed with all its dependencies, since I read that it can do masking and *ab initi ...
written 6 weeks ago by maxwhjohn198840
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Eukaryotic Genome Annotation - Without ESTs or Transcriptomic or Proteomic Data
... First off, **apologies if this is a duplicate** - I have searched and not found anything addressing this question, but that doesn't mean this hasn't been asked elsewhere. I have a genome assembly, and I want to annotate some contigs of interest. The species in question is not well-studied and ther ...
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Comment: C: Help me choose an assembler (for something quite specific)
... Thanks - yes, I'm also dubious about whether I will be able to make any improvements. I am currently trying to get outputs from nucmer in an intelligible graphical format, after doing exactly what you suggest :) ...
written 8 weeks ago by maxwhjohn198840
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Comment: C: Help me choose an assembler (for something quite specific)
... Thanks for the correction! You are quite correct, I had completely forgotten about that option. Much appreciated, I might give this a try. ...
written 8 weeks ago by maxwhjohn198840
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Help me choose an assembler (for something quite specific)
... I have a *de novo* assembly, produced with w2rap-contigger (a forked version of Discovar DeNovo, made at the Earlham Institute) from a single PE library. The assembly is not great (N50 ~ 55 kb) but it's not totally useless for me. I am fishing for contigs of interest, and I am getting some good r ...
genome assembly next-gen written 9 weeks ago by maxwhjohn198840 • updated 8 weeks ago by colindaven420
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Answer: A: Merging two split contigs
... Just an idea - not sure whether it would work - but you could try providing your contigs to Canu as long read sequences to be assembled, and see if it stitches those which overlap, as you described, back together. I'm trying to think of reasons why this could happen - might there have been some mat ...
written 10 weeks ago by maxwhjohn198840
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Answer: A: Doubt about specifying options in SPAdes
... Try: spades.py --s1 input.fastq ... ...
written 11 weeks ago by maxwhjohn198840
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Comment: C: DiscovarDenovo - fastq files should be interlaced
... I think when you provide Discovar De Novo with a single read file, it expects that the only reason you would do this is because the file in question is an interleaved read file. ...
written 11 weeks ago by maxwhjohn198840

Latest awards to maxwhjohn1988

Scholar 10 weeks ago, created an answer that has been accepted. For A: Discovar De Novo assembly - "Attempt to allocate memory failed"
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: DiscovarDenovo - fastq files should be interlaced
Scholar 11 weeks ago, created an answer that has been accepted. For A: Discovar De Novo assembly - "Attempt to allocate memory failed"

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