User: rthapa
rthapa • 40
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Posts by rthapa
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... 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
rthapa • 40
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... I used canu for genome assembly. ...
written 4 weeks ago by
rthapa • 40
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... 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 ...
written 4 weeks ago by
rthapa • 40
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... 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 ...
written 8 weeks ago by
rthapa • 40
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... 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
rthapa • 40
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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
rthapa • 40
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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
rthapa • 40
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... 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 ...
written 9 weeks ago by
rthapa • 40
• updated
9 weeks ago by
hugo.avila • 160
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... 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 ...
written 10 weeks ago by
rthapa • 40
• updated
10 weeks ago by
khalid.belkhir • 30
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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
rthapa • 40
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For transcript count after string tie merge
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