User: rthapa

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rthapa40
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Posts by rthapa

<prev • 68 results • page 1 of 7 • next >
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Comment: C: bacterial genome assembly with nano pore sequence data
... Here is the results of contig stats for the contigs with large number of contigs A C G T N IUPAC Other GC GC_stdev 0.2318 0.2686 0.2677 0.2319 0.0000 0.0000 0.0000 0.5363 0.0594 Main genome scaffold total: 9 Main genome contig total: 9 Main genome scaffo ...
written 4 weeks ago by rthapa40
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Comment: C: bacterial genome assembly with nano pore sequence data
... I used canu for genome assembly. ...
written 4 weeks ago by rthapa40
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bacterial genome assembly with nano pore sequence data
... Hi, I am doing genome assembly of different bacterial strains with barcoded nanopore sequenced reads. The genome size of the bacteria is 3.8Mb. After genome assembly, I am getting 2 contigs with longest contig length of 3.6 Mb for one strain and 9 contigs with 1.5 Mb contig length for another strai ...
assembly nanopore written 4 weeks ago by rthapa40
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Vst estimation across different populations from copy number data
... Hi, I want to estimate Vst value across different population based on the copy number data. I have 5 populations and in each population, I have 10 samples. I wonder in order to estimate Vst values, do I need to average the CN values across samples from each population and then compare across the pop ...
genome copy number vst written 8 weeks ago by rthapa40
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Comment: C: Obtain gene names for the SNPs from GWAS result
... I think you should be able to use bedtools to intersect SNP position with annotation file and get the gene names. ...
written 8 weeks ago by rthapa40
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Comment: C: mauve for contigs
... Thank you for the suggestion. That is really helpful. I have QUAST report. How could we decide if we need to make a scaffold from the contigs or just proceed with the largest contig? I checked among the contigs and found that the smallest contig is a plasmid. Assembly ea.contigs # contigs ( ...
written 8 weeks ago by rthapa40
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Comment: C: mauve for contigs
... Thank you for your suggestions. Yes, it is a bacterial genome from Erwinia spp. I don't have a QUAST report to share for now. I have a question regarding QUAST. From the script, it looks like the contigs should be in separate files and also it seems like we need a annotation file too. I have a singl ...
written 9 weeks ago by rthapa40
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mauve for contigs
... Hi, I am new to genome assembly. I have got 6 contigs after genome assembly. I wonder if I need to use all 6 contigs to merge into one with tools like mauve to get one contig or could I proceed with the longest contig for alignment with reference sequence? I would appreciate any suggestion. Thanks ...
genome mauve written 9 weeks ago by rthapa40 • updated 9 weeks ago by hugo.avila160
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Copy number variation data for population structure analysis
... Hi, Does anyone have any idea if there is any tool available to detect population structure from copy number data rather than SNP data? Thanks ...
cnv written 10 weeks ago by rthapa40 • updated 10 weeks ago by khalid.belkhir30
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Comment: C: B allele frequency (BAF)
... Thanks a lot but the genome I am using is not the human genome. ...
written 11 weeks ago by rthapa40

Latest awards to rthapa

Popular Question 5 weeks ago, created a question with more than 1,000 views. For best value of lfc threshold
Popular Question 5 weeks ago, created a question with more than 1,000 views. For best value of lfc threshold
Popular Question 12 months ago, created a question with more than 1,000 views. For best value of lfc threshold
Popular Question 19 months ago, created a question with more than 1,000 views. For transcript count after string tie merge

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