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What metrics to use to calculate variant library evenness or uniformity or bias
library-bias variant
updated 13 months ago by 44k • written 13 months ago by ▴ 90
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409
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what is the impact of 10% contamination in bacterial growth experiment in downstream analysis?
bacterial contamination assay experiment
19 months ago by eli_bayat ▴ 90
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1.0k
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Comment: Comment: bbmerge high percentage of no solution reads
24 months ago by eli_bayat ▴ 90
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1.0k
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Comment: Comment: bbmerge high percentage of no solution reads
24 months ago by eli_bayat ▴ 90
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5
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1.0k
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bbmerge high percentage of no solution reads
no_solution BBmerge sequencing merg
updated 24 months ago by 146k • written 24 months ago by ▴ 90
2
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1
reply
494
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what can cause high(> 80%) spike-ins and low read count (<100 reads) in low complexity ampseq run
amplicon_sequencing NGS_reads low_complexity spike-ins ampseq
updated 2.2 years ago by 4.3k • written 2.2 years ago by ▴ 90
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1.3k
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Comment: Comment: How to calculate percentage of chimeras from r1/r2 files
2.4 years ago by eli_bayat ▴ 90
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1
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1.8k
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Comment: Comment: How to find corresponding variant position in a bacteria where the variant was r
2.4 years ago by eli_bayat ▴ 90
2
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3
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1.8k
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How to find corresponding variant position in a bacteria where the variant was reported according to the E.coli numbering system?
bacteria Ecoli_numbering_system variants mutations
updated 2.4 years ago by • 0 • written 3.0 years ago by ▴ 90
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1.3k
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Comment: Comment: How to calculate percentage of chimeras from r1/r2 files
2.4 years ago by eli_bayat ▴ 90
2
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5
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1.3k
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How to calculate percentage of chimeras from r1/r2 files
paired-end-reads chimeric sequences usearch chimera
updated 2.4 years ago by 10k • written 2.5 years ago by ▴ 90
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1.1k
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Comment: Comment: Adding flanking regions to a gene for primer design
2.8 years ago by eli_bayat ▴ 90
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2
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1.1k
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Adding flanking regions to a gene for primer design
primer_design flanking amplicon primer3 flanking_region
2.8 years ago by eli_bayat ▴ 90
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0
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469
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different alignment based insert size and tapestation fragmentation size
fragmentation_size bwa-mem_alignment insert_size tapestation_fragmentation_trace
2.9 years ago by eli_bayat ▴ 90
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0
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993
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Comment: Comment: how to design primer with primer3 and what parameters are necessary to feed to p
2.9 years ago by eli_bayat ▴ 90
2
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2
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993
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how to design primer with primer3 and what parameters are necessary to feed to primer3
primer_design design primers primer3
2.9 years ago by eli_bayat ▴ 90
0
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1
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1.6k
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Comment: Comment: how to generate reference genome from paired-end reads
2.9 years ago by eli_bayat ▴ 90
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1
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1.6k
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Comment: Comment: how to generate reference genome from paired-end reads
2.9 years ago by eli_bayat ▴ 90
3
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5
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1.6k
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How to find the mutations of a bacterium without reference genome from paired-end short-reads?
reference paired-end-reads consensus genome
updated 2.9 years ago by 8.7k • written 2.9 years ago by ▴ 90
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0
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2.1k
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Comment: Comment: [bam_sort_core] merging from 32 files and 16 in-memory blocks... samtools sort:
3.0 years ago by eli_bayat ▴ 90
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2
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2.1k
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[bam_sort_core] merging from 32 files and 16 in-memory blocks... samtools sort: failed to write header to "-"
samtools pacbio
updated 17 months ago by 44k • written 3.0 years ago by ▴ 90
1
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1
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763
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how confident we are if a read aligned to 23S belong to the bacteria of interest and not other bacteria in the same region that are in our sample?
universal_genes bwa alignment
updated 3.0 years ago by ★ 28k • written 3.0 years ago by ▴ 90
2
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1
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1.3k
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QC metrics from pacbio long reads data
coverage QC Long_Reads smrtlink Pacbio
updated 3.0 years ago by ▴ 410 • written 3.0 years ago by ▴ 90
0
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0
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493
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How to find adapter dimer present in a library from reads?
adapter_dimer Library
updated 16 months ago by 44k • written 3.1 years ago by ▴ 90
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0
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1.8k
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Comment: Comment: converting Bam to fastq while removing clipping(hard/soft clip bases)
3.1 years ago by eli_bayat ▴ 90
1
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2
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1.8k
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converting Bam to fastq while removing clipping(hard/soft clip bases)
Soft-clipping fastq hard-clipping bam
updated 16 months ago by 44k • written 3.1 years ago by ▴ 90
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0
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1.7k
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Comment: Comment: Any suggestion on metagenomics pipelines for processing shotgun metagenomics who
3.1 years ago by eli_bayat ▴ 90
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0
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1.7k
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Comment: Comment: Any suggestion on metagenomics pipelines for processing shotgun metagenomics who
3.1 years ago by eli_bayat ▴ 90
2
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4
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1.7k
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Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?
metagenomics_pipelines WGS shotgun_metagenomics antimicrobial_resistance
3.1 years ago by eli_bayat ▴ 90
0
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1
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1.9k
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Comment: Comment: Genomic landscape of Neisseria gonorrhoeae wild-type strain whole genome schema
3.2 years ago by eli_bayat ▴ 90
0
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1
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1.9k
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Comment: Comment: Genomic landscape of Neisseria gonorrhoeae wild-type strain whole genome schema
3.2 years ago by eli_bayat ▴ 90
0
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1
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1.9k
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Comment: Comment: Genomic landscape of Neisseria gonorrhoeae wild-type strain whole genome schema
3.2 years ago by eli_bayat ▴ 90
5
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7
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1.9k
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Genomic landscape of Neisseria gonorrhoeae wild-type strain whole genome schematic.
Figures Neisseria_gonorrhoeae regions whole_genome Strain
updated 3.2 years ago by 146k • written 3.2 years ago by ▴ 90
0
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0
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451
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Find the copy number of marker genes and the number of them that results in drug resistance?
copy-number 23SrRNA marker-gene drug-Resistance
3.2 years ago by eli_bayat ▴ 90
0
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0
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918
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Comment: Comment: How to find the number of copies of genes (e.g. 23S rRNA) present in a genome?
3.2 years ago by eli_bayat ▴ 90
1
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2
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918
views
How to find the number of copies of genes (e.g. 23S rRNA) present in a genome?
antimicrobial-resistance reference-database copies-of-genes metadata NCBI
3.2 years ago by eli_bayat ▴ 90
4
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3
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1.2k
views
Finding metagenomic short read sequences
antimicrobial reference short sequences reads data metagenomic resistance
updated 3.3 years ago by ★ 1.1k • written 3.3 years ago by ▴ 90
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0
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1.6k
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Comment: Comment: identifying strain using pangolin and nextclade
3.6 years ago by eli_bayat ▴ 90
1
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2
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1.6k
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identifying strain using pangolin and nextclade
Covid19 pangolin nextstrain strain nextclade
3.6 years ago by eli_bayat ▴ 90
0
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0
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1.5k
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Comment: Comment: SARS-CoV2 strain identifying strain
3.6 years ago by eli_bayat ▴ 90
0
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0
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1.5k
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Comment: Comment: SARS-CoV2 strain identifying strain
3.6 years ago by eli_bayat ▴ 90
7
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4
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1.5k
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SARS-CoV2 strain identifying strain
Covid19 SARS-CoV-2 GISAid
updated 9 months ago by 44k • written 3.6 years ago by ▴ 90
0
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1
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1.1k
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Comment: C: blastn --remote option skipping sequences
4.1 years ago by eli_bayat ▴ 90
0
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0
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1.1k
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Comment: C: blastn --remote option skipping sequences
4.1 years ago by eli_bayat ▴ 90
0
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5
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1.1k
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blastn --remote option skipping sequences
command-line blast
4.1 years ago by eli_bayat ▴ 90
2
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2
replies
926
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How to get Positive Control gut or Vaginal microbiome dataset
Positive control decontamination filtering
updated 4.6 years ago by 20 • written 4.8 years ago by ▴ 90
1
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1
reply
558
views
How to find genes and function of particular species such as Lactobacillus Crispatus?
KEEG Pathway functions bacteria gene
updated 4.7 years ago by 146k • written 4.7 years ago by ▴ 90
3
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3
replies
1.1k
views
How to find a pathway from bacteria to disease
gene pathways KEEG disease bacteria
updated 4.8 years ago by ▴ 1000 • written 4.8 years ago by ▴ 90
0
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0
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1.1k
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Comment: C: How to find a pathway from genes to disease
4.8 years ago by eli_bayat ▴ 90
0
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0
replies
8.9k
views
Comment: C: How to Demultiplex a fastq.gz file.
5.2 years ago by eli_bayat ▴ 90
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