User: Beuss

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Beuss100
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100
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Location:
France
Last seen:
29 minutes ago
Joined:
3 years, 5 months ago
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Posts by Beuss

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Can I make GFF3 from either GFF or genome fasta file?
... I guess the format of example has been broken, so I suppose that your input file is like this: Bf_V2_1 1 797 - bf_rep_71 Unknown Bf_V2_1 848 936 + (TA)n Simple_repeat Bf_V2_1 1236 1369 - CR1-11_BF LINE/CR1 Bf_V2_1 2151 2171 + (TA)n Simple_repeat Bf_V2_1 2351 3238 - bf_rep_71 Un ...
written 5 weeks ago by Beuss100
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Comment: C: Assembly of wheat genome
... It seem to be interesting, thank for the ref. ...
written 5 weeks ago by Beuss100
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Comment: C: Minia: Pool allocation failed for 68766984 bytes (kmers alloc), mainbuffer is nu
... Ok the problem is sovled ! Thanks again. ...
written 8 weeks ago by Beuss100
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Comment: C: Minia: Pool allocation failed for 68766984 bytes (kmers alloc), mainbuffer is nu
... Thank for the advise ! It will be applied for the next runs. ...
written 8 weeks ago by Beuss100
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Comment: C: Minia: Pool allocation failed for 68766984 bytes (kmers alloc), mainbuffer is nu
... Hi, I'm think your are right. Before your answer, I launched new assemblies with the -max-memory option set to 0 (no limit I presumed). For now, 3 of the 5 assemblies that I launched finished with no problems. I'm waiting for the results of the two last before confirming the solution. Thank y ...
written 8 weeks ago by Beuss100
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Minia: Pool allocation failed for 68766984 bytes (kmers alloc), mainbuffer is null?.
... Hello, I'm trying to assemble a plant genome (1.1 Gbp) from 38 illumina reads datasets (pair end and mate pair) with a coverage of 150x. The version of Minia that I use is : Minia 3, git commit 67ac2ad. The parameters used are : minia -in inMinia.txt -out plant_79 -kmer-size 79 -ma ...
assembly minia written 8 weeks ago by Beuss100 • updated 8 weeks ago by guillaume.rizk40
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Comment: A: How to use ALLPATH-LG assembler
... Take a look to DISCOVAR denovo and MaSuRCA : https://software.broadinstitute.org/software/discovar/blog/ http://masurca.blogspot.com/ ...
written 3 months ago by Beuss100
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Comment: C: How to annotate repeats?
... You're welcome. Do not hesitate if you have any other questions. ...
written 5 months ago by Beuss100
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Answer: A: How to annotate repeats?
... Hi, As usual, all depend of which question you to answer. I you want an idea of the global quantity of repeat for your genome, a quick annotation with RepeatMasker/Repbase can be enough. Or there a public annotation layer already available ? But in your case, because you are searching for a lin ...
written 5 months ago by Beuss100
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Answer: A: Using DRMAA in bioinformatics workflows?
... Hi, Since i'm doing bioinformatic on clusters, I never needed to use DRMAA. I always used the scheduler commands in my workflow for managing jobs. The only time I had to use DRMAA ([slurm-drmaa][1]), was when moved our cluster to SLURM to made the galaxy server able to submit job. I would be a ...
written 10 months ago by Beuss100

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