User: maxwhjohn1988

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Posts by maxwhjohn1988

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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 2 days 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 2 days 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 6 days ago by maxwhjohn198840 • updated 5 days ago by colindaven340
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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 16 days ago by maxwhjohn198840
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Answer: A: Doubt about specifying options in SPAdes
... Try: spades.py --s1 input.fastq ... ...
written 20 days 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 20 days ago by maxwhjohn198840
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Answer: A: DiscovarDenovo - fastq files should be interlaced
... Sounds like you have an odd number of reads in your input fastq file. Discovar De Novo is designed to work with paired-end data (with a specific read length) - you should have an even number of reads if you've got paired-end reads. I'm not too familiar with TruSeq but the file name with "LongRead" ...
written 20 days ago by maxwhjohn198840
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Answer: A: Discovar De Novo assembly - "Attempt to allocate memory failed"
... For anyone looking at this post, who has the same problem: I have it fixed now. I was pointed at a forked version of Discovar, developed by a group at the Earlham Institute in Norwich. They wanted to use Discovar De Novo to assemble a wheat genome and it just crashed, so they got into it and fiddl ...
written 22 days ago by maxwhjohn198840
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Comment: C: Can I use BLASTn to only return hits which start with a perfect match to a parti
... Hi again Yes, I used Stacks to process my RADseq reads. I'm using pooled samples though so there's only so far I can go with Stacks. I have actually got the results I needed from USEARCH's ublast now. I used this command: usearch -ublast RADreads.fa -db assembly.fa -evalue 1.0e-20 -strand ...
written 7 weeks ago by maxwhjohn198840
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Comment: C: Can I use BLASTn to only return hits which start with a perfect match to a parti
... Hi st.ph.n Sorry I couldn't reply earlier, as a new user BioStars limits the number of posts I can make every day (which includes replies!) Either I'm misunderstanding something, or I haven't explained myself very well. I'll try to be more explicit; maybe I'll suddenly understand that what you ar ...
written 7 weeks ago by maxwhjohn198840

Latest awards to maxwhjohn1988

Scholar 14 days ago, created an answer that has been accepted. For A: Discovar De Novo assembly - "Attempt to allocate memory failed"
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: DiscovarDenovo - fastq files should be interlaced
Scholar 22 days ago, created an answer that has been accepted. For A: Discovar De Novo assembly - "Attempt to allocate memory failed"

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