User: rthapa

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rthapa40
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r*****@tamu.edu

Posts by rthapa

<prev • 102 results • page 1 of 11 • next >
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Identification of presence of genes by aligning the illumina reads to reference genome with Geneious
... Hi, I am trying to find if the particular gene is present in the illumina reads. I have gene sequence for this particular gene. I tried using Geneious software for aligning the illumina reads to the gene sequence but the Geneious sent a message that there is no contig. I wonder if that is because th ...
alignment geneious mapping written 1 day ago by rthapa40
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finding coverage of particular gene sequence from illumina short reads
... Hi, I want to find the coverage of a particular gene from the illumina reads. I have the protein sequence of this gene. Does anyone have suggestion what would be the best approach? Thanks ...
illumina coverage written 3 days ago by rthapa40
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Comment: C: Whole-genome alignment of two or more bacterial genomes - find structural varian
... Hi, did you find your answer? ...
written 11 days ago by rthapa40
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Comment: C: mummer dot plot
... Hi Alex, Do we need to change the orientation and starting point of the genome assembly of bacteria before using mummer to check SNPs and INDELs? ...
written 16 days ago by rthapa40
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Comment: C: MUMmer plot visualization
... Thank you. But when I check the mummer results for structural variation, there are four inversion in the assembly compared to reference genome. I wonder why mummer plot is showing only two inversions. tig00000001 INV 228534 226344 -2189 tig00000001 GAP 745271 742507 -2763 -232 -2531 tig ...
written 18 days ago by rthapa40
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Comment: C: MUMmer plot visualization
... It looks like the reverse complement is better to visualize. It seems like there are two inversions in the assembled genome https://ibb.co/k5MqYqZ. ![enter image description here][1] Is the red bar present in the right corner duplicated region in the reference genome? Do you have any idea if I need ...
written 18 days ago by rthapa40 • updated 18 days ago by GenoMax96k
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Comment: C: MUMmer plot visualization
... No, I did't try the reverse complement. Do you have any suggestion on tools that we can use for getting reverse complement? The alignment looks like https://ibb.co/cL6ydYr with mauve. ![enter image description here][1] [1]: https://i.ibb.co/NS9FzTy/Screen-Shot-2021-02-11-at-2-38-12-PM.png ...
written 18 days ago by rthapa40 • updated 18 days ago by GenoMax96k
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MUMmer plot visualization
... Hi, I am using MUMmer plot to compare between a de novo assembly with reference genome. The percent identity between two genomes is more than 99% but when I plot the two genomes with MUMmer plot, the plot (https://ibb.co/q08xsZw) doesn't look like that. Does anyone have any idea? Thanks ![enter ima ...
mummer plot written 18 days ago by rthapa40 • updated 18 days ago by GenoMax96k
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MUMmer for structural variant call
... Hi, I want to call structural variants from bacterial genome by comparing the de novo assembly with reference genome. Do I need to fix the start point of the genome with circlator before calling SV with MUMmer? I would appreciate any suggestions. Thanks ...
structural variants circlator mummer written 18 days ago by rthapa40
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Comment: C: Rotate circular contigs to replication initiator protein (ex. dnaA, repA)
... Thank you. Did you try calling structural variants after fixing the start point. If so did you use mauve for calling SV? ...
written 18 days ago by rthapa40

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Centurion 3 days ago, created 100 posts.
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