User: maxwhjohn1988

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Posts by maxwhjohn1988

<prev • 33 results • page 1 of 4 • next >
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Answer: A: Glimmer 3 multi-extract input problem
... Sorry for bumping an old thread, but I found it while suffering a similar problem to the original poster, and found something of a solution, which I thought worth sharing. Note that this answer doesn't address the specific problem of getting Glimmer to do this job, but it does address the issue of ...
written 22 days ago by maxwhjohn198840
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Comment: C: merging 10X genomics assemblies
... How did you get on with CAMSA? I'm in the same boat and looking around for tools written to do this job (I could knock something up myself but why re-invent the wheel, right?) ...
written 25 days ago by maxwhjohn198840
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Comment: C: Enhancing draft genome using 10X data
... Hi Mostafa (Apologies first for posting this here, I can't work out how to send you a private message directly). I want to use ARCS to scaffold a draft genome. I have the program installed but its documentation is too minimal for me to get going. So far I have made an interleaved fastq file of my ...
written 6 weeks ago by maxwhjohn198840
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Comment: C: Are there any de novo assemblers which can handle (either) transcriptomic or gen
... Just thought I'd provide an update (might be helpful for anyone else reading this in the future). I abandoned my idea of a single piece of software for all cases. For a quick and dirty de novo transcriptome assembly I have settled on SOAPdenovo-Trans. It's not packaged with SOAPdenovo but is base ...
written 3 months ago by maxwhjohn198840
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Comment: C: Are there any de novo assemblers which can handle (either) transcriptomic or gen
... Thanks I'll check out Abyss with some toy data. Much appreciated. ...
written 4 months ago by maxwhjohn198840
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Are there any de novo assemblers which can handle (either) transcriptomic or genomic reads?
... I'm looking to make some proposals for QC pipelines for a range of sequencing applications. Two of the applications I'm thinking about are genome sequencing and transcriptome sequencing. When a reference is not available, a quick and dirty assembly is desirable to map reads to. I wondered if anyo ...
assembly rna dna written 4 months ago by maxwhjohn198840 • updated 4 months ago by Damian Kao15k
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Comment: C: Edgeredef Failed When Running Repeatmodeler
... Hi @tuentje.peeters - so sorry for not seeing this before. No, I did not, I think I moved on to do something else. It looks like @WDbakker, below, has succeeded in getting around the problem. ...
written 4 months ago by maxwhjohn198840
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Answer: A: Repeatmodeler Error (Eleredef)
... I am using RECON as standalone, and I'm seeing this same error. Sorry to bump such an old thread, but has anyone got a solution to this? FYI I'm using RECON 1.08 ...
written 9 months ago by maxwhjohn198840
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Answer: A: Edgeredef Failed When Running Repeatmodeler
... Sorry to bump such an old thread, but I have the same issue. I'm running RECON as a standalone. I've got the same exit code from both versions of RECON (1.05 and 1.08). This is my command: perl /home/m/mwhj1/2018/programs/RECON-1.08/scripts/recon.pl a.lines.seqlist.txt \ > whole_asse ...
written 9 months ago by maxwhjohn198840
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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 13 months ago by maxwhjohn198840

Latest awards to maxwhjohn1988

Scholar 14 months ago, created an answer that has been accepted. For A: Discovar De Novo assembly - "Attempt to allocate memory failed"
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: DiscovarDenovo - fastq files should be interlaced
Scholar 14 months ago, created an answer that has been accepted. For A: Discovar De Novo assembly - "Attempt to allocate memory failed"

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