User: David

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David150
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Posts by David

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Comment: C: What is the symmetric identity percent
... Sorry, i have updated the image ...
written 4 weeks ago by David150
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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 weeks ago by David150
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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 4 months ago by David150
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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 4 months ago by David150
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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 4 months ago by David150 • updated 4 months ago by RamRS21k
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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 4 months ago by David150
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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 4 months ago by David150
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IGV alignment explanation
... Hello, This is the IGV view from reads illumina mapped to a reference bacterial genome. The window shows a specific bacterial gene. Each sample is a gut profile from a donnor. (WGS illumina). In the upper sample i see red, blue and green vertical lines in some of the reads for a particular positi ...
bam igv written 4 months ago by David150 • updated 4 months ago by h.mon25k
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Pathway enrichment analysis bacterial genome
... Hi, I have created a counts matrix from an experiment with 20 bacterial samples (10 bacteria treated and 10 not treated). I would like to identify the pathways that over and under represented upon treatment. So far i have created a counts matrix as follows. Each row represents an EC number found ...
metacyc R david kegg clusterprofiler written 4 months ago by David150 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Gene coverage from Bam files
... Thanks, Indeed the following command did work: > bedtools coverage -hist -b 1.mapped.bam.sorted -a genome.map.bed > > Sample.hist ...
written 5 months ago by David150

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