User: Beuss

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Beuss110
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110
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Location:
France
Last seen:
5 months, 1 week ago
Joined:
4 years, 6 months ago
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Posts by Beuss

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Pipeline transposable elements
... RepeatMasker is a viable solution if you already have a database of TEs from a very close specie. With RepeatMasker and Repbase, you won't be able to detect all mobile elements specific to your newly assembled genome. Moreover, your annotation will be polluted by false positive. REPET perform de ...
written 5 months ago by Beuss110
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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 15 months ago by Beuss110
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Comment: C: Assembly of wheat genome
... It seem to be interesting, thank for the ref. ...
written 15 months ago by Beuss110
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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 15 months ago by Beuss110
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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 15 months ago by Beuss110
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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 15 months ago by Beuss110
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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 15 months ago by Beuss110 • updated 15 months 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 17 months ago by Beuss110
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Comment: C: How to annotate repeats?
... You're welcome. Do not hesitate if you have any other questions. ...
written 19 months ago by Beuss110
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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 19 months ago by Beuss110

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