User: StudentBio

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StudentBio0
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Posts by StudentBio

<prev • 21 results • page 1 of 3 • next >
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solution for SPades to assemble genome with low quality data
... hello the community when I run spades with this command: inra@inra-VirtualBox:~/SPAdes-3.5.0-Linux/bin$ ./spades.py --sc -m 4 --iontorrent -k 21,33,55,77,99,127 -s /home/inra/share/outils/trimmed.fastq -o /home/inra/share/spades i get this error, please any suggestions, i have single-reads fro ...
assembly ion-torrent spades single-end written 3 days ago by StudentBio0 • updated 2 days ago by Sej Modha3.1k
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Comment: C: kmergenie does not predicted a best k value
... i'm sorry but i dont know how i can expect genome size and ploidy, and target sequencing coverage and this for what i'm trying to find the best K for use Genomescope qui (detecting the genome characteristics) according to fastqc report: Sequence length 20-397 and %GC 42 about my reads i trimmed t ...
written 13 days ago by StudentBio0
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kmergenie does not predicted a best k value
... hi please, I am trying out kmergenie to determine optimal kmer values for phoenix dactylifera genome assembly. and i get this error any suggestion please ./kmergenie /home/vshare/outils/trimmed.fastq --diploid running histogram estimation Setting maximum kmer length to: 133 ...
assembly kmergenie written 13 days ago by StudentBio0 • updated 13 days ago by h.mon16k
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tool to estimate the characteristics of my palm date genome
... Hello please if anyone can recommend me a tool to estimate the characteristics of the palm date genome from the reads. for genomescope I found that it is effective for haploid genomes as long as the date palm genome is diploid ... ...
genomescope date palm written 15 days ago by StudentBio0
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Comment: C: efficient algorithm for de novo assembly using de bruijn graph
... phoenix dactylifera genome length 22 953 390 bp ; het 4,25% ...
written 15 days ago by StudentBio0
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efficient algorithm for de novo assembly using de bruijn graph
... hello everebody please I am trying to assemble my reads using an algorithms for de novo assembly( De Bruijn Graph) and I don t know which algorith de novo more efficient in my case the optimal k using kmergenie is 17 Read Data : Ion Torrent, single end, percentage of GC 42, sequence length bet ...
assembly date palm de bruijn k-mers written 15 days ago by StudentBio0 • updated 10 days ago by colindaven740
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Comment: C: genomescope profile failed to converge
... thanks of you all i can resolve it removing the -C option from jellyfish and it worked jellyfish count -m 17 -s 1000000000 -t 10 /home/vshare/bowtie2/trimmed.fastq -o reads2.jf ...
written 16 days ago by StudentBio0
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Comment: C: genomescope profile failed to converge
... I removed the -C option from jellyfish and it worked thank you very much jellyfish count -m 17 -s 1000000000 -t 10 /home/vshare/bowtie2/trimmed.fastq -o reads2.jf ...
written 16 days ago by StudentBio0
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genomescope profile failed to converge
... hello the community, to estimate the characteristics of my genome I used GenomeScope, as a result I got an error like GenomeScope profile failed to converge and depending on what i found the problem is because low coverage or low quality reads ....so please if anyone can help me to solve this thi ...
genomescope k-mers jellyfish written 16 days ago by StudentBio0 • updated 16 days ago by lieven.sterck1.9k
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Comment: C: choice of k value for mapping my reads again a reference genome
... i have read sizes between 25-403 and total sequence about 89 000 000 and size of the genome is about 295 000 000 please which kmer value I must adopt ...
written 17 days ago by StudentBio0

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