User: David

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David160
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Posts by David

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Answer: A: mummer dot plot
... Hi Alex, Definetly you are right (thanks for the figure)!!!!! Let me add more info to the discussion. The two genomes have been assembled from the same input pacbio dataset (RSII). The only difference is that one was assembled 3 years ago and the other yesterday with Flye. WOuld there be any expl ...
written 8 days ago by David160
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Answer: A: mummer dot plot
... Thanks Alex, these are complete genomes. A quick blast shows that the longer fragment matches plus/minus to the reference. And the small fragment also blast in plus/minus compared to the reference. However i would expect a single fragment and not two. This suggests that the small fragment is also re ...
written 9 days ago by David160
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mummer dot plot
... Hello, I have aligned two complete bacterial genomes using mummer (1 contig per genome) I´m not sure i understand well the output. Here is the mummer plot: I think the plot suggest that there are two main reverse regions. Is that correct. If so is this what is happening at the genome level. Tr ...
dotplot mummer written 9 days ago by David160
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Comment: C: What is the symmetric identity percent
... Sorry, i have updated the image ...
written 4 months ago by David160
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What is the symmetric identity percent
... Hi, Any idea what the symmetric identity % is vs gapped identity is for a genome assembly ?? As shown for this entry: https://www.ncbi.nlm.nih.gov/genome/neighbors/152?genome_assembly_id=260322 ![Image][1] [1]: https://i.ibb.co/kDDpjGf/Screenshot-2019-05-15-at-17-20-39.png ...
genome identity written 4 months ago by David160
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Comment: C: haplotypeCaller groups comparison
... Great Thanks. Once you obtain the vcf file how would you compare the two groups (normal vs treated) ? Thanks ...
written 7 months ago by David160
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haplotypeCaller groups comparison
... Hi, I´m trying to identify variants from two groups composed of 25 samples (12 samples for the control and 12 samples for the treatment). I´m using HaplotypeCaller as follows. My reference genome is a bacterial genome. All my samples are haploid. gatk HaplotypeCaller --native-pair-hmm-threads ...
gatk written 7 months ago by David160
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Answer: A: Identify deletion in multiple bam files compared to the same bacterial reference
... Thanks for the answer, i have tried as follows samtools view -b your_file.bam "sequence1:345000-345510" > hits_file.bam Then to count how many reads have at least the deletion i have done: samtools view 17.mapped_sorted.bam "sequence1:345000-345510" | grep -cE '[0-9]{1,2}D' 20 ...
written 7 months ago by David160 • updated 7 months ago by RamRS24k
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Identify deletion in multiple bam files compared to the same bacterial reference
... Hi, I have done an illumina WGS experiment in many gut samples and mapped those samples back to a reference bacterial genome. I have identified a small deletion (2bp) in one bam file compared to the reference bacterial genome. I have the coordinates of the region. Is there a quick way to chech if ...
bedtools bam written 7 months ago by David160
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Comment: C: IGV alignment explanation
... Thanks @h.mon . The reference genome is a hybrid assembly (illumina + nanopore) which is probably why it looks so good. short reads were mapped back to the assembly. Indeed i think i have two strains mapping to the reference genome which could explain the phenotype i observe in the individuals gu ...
written 7 months ago by David160

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