User: David

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David140
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Posts by David

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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 days ago by David140
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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 days ago by David140
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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 8 days ago by David140 • updated 8 days ago by RamRS20k
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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 8 days ago by David140
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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 25 days ago by David140
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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 25 days ago by David140 • updated 25 days ago by h.mon23k
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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 28 days ago by David140
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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 4 weeks ago by David140
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Gene coverage from Bam files
... Hi, I would like to extract gene coverage from a bacterial genome that i have assembled. I have done the following steps: I have created a bed file with all genes i´m interested in from my gff file (corresponding to my assembled genome. Only 1 full chromosome). My bed file is **genome.map.bed**. ...
bedtools written 4 weeks ago by David140 • updated 4 weeks ago by finswimmer9.9k
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Comment: C: Relative abundance fro metagenomics samples
... What i did was to map reads back to each of the bins so you get the bin coverage. Assuming your bin corresponds to one genome you get an approximate number of copies. ...
written 5 weeks ago by David140

Latest awards to David

Popular Question 4 days ago, created a question with more than 1,000 views. For Normalization methods for metagenomics WGS data (not 16S data)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Download NCBI genomes using taxonomy id (taxid)
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Download NCBI genomes using taxonomy id (taxid)
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Popular Question 10 months ago, created a question with more than 1,000 views. For Contigs Taxonomy from assembled metagenomes
Popular Question 10 months ago, created a question with more than 1,000 views. For Scaffolding for metagenomics
Popular Question 10 months ago, created a question with more than 1,000 views. For Normalize bedtools gene coverage by total number of reads
Popular Question 10 months ago, created a question with more than 1,000 views. For Get phylogenetic tree from abundance table
Popular Question 10 months ago, created a question with more than 1,000 views. For Parse fasta header with regex in python
Popular Question 10 months ago, created a question with more than 1,000 views. For fastqc gc-content peak and adapter content
Popular Question 10 months ago, created a question with more than 1,000 views. For Relative abundance fro metagenomics samples
Popular Question 10 months ago, created a question with more than 1,000 views. For Relative abundance fro metagenomics samples
Student 21 months ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)
Student 23 months ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)

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