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0
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329
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What metrics to use to calculate variant library evenness or uniformity or bias
library-bias variant
updated 8 months ago by 43k • written 8 months ago by ▴ 90
0
votes
0
replies
345
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what is the impact of 10% contamination in bacterial growth experiment in downstream analysis?
bacterial contamination assay experiment
13 months ago by eli_bayat ▴ 90
1
vote
5
replies
859
views
bbmerge high percentage of no solution reads
no_solution BBmerge sequencing merg
updated 18 months ago by 142k • written 18 months ago by ▴ 90
2
votes
1
reply
426
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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 21 months ago by 3.9k • written 21 months ago by ▴ 90
2
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3
replies
1.7k
views
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 23 months ago by • 0 • written 2.5 years ago by ▴ 90
2
votes
5
replies
1.1k
views
How to calculate percentage of chimeras from r1/r2 files
paired-end-reads chimeric sequences usearch chimera
updated 23 months ago by 10k • written 24 months ago by ▴ 90
0
votes
2
replies
849
views
Adding flanking regions to a gene for primer design
primer_design flanking amplicon primer3 flanking_region
2.4 years ago by eli_bayat ▴ 90
0
votes
0
replies
419
views
different alignment based insert size and tapestation fragmentation size
fragmentation_size bwa-mem_alignment insert_size tapestation_fragmentation_trace
2.4 years ago by eli_bayat ▴ 90
2
votes
2
replies
902
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how to design primer with primer3 and what parameters are necessary to feed to primer3
primer_design design primers primer3
2.4 years ago by eli_bayat ▴ 90
3
votes
5
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1.4k
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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 2.4 years ago by 8.5k • written 2.4 years ago by ▴ 90
1
vote
2
replies
2.0k
views
[bam_sort_core] merging from 32 files and 16 in-memory blocks... samtools sort: failed to write header to "-"
samtools pacbio
updated 12 months ago by 43k • written 2.6 years ago by ▴ 90
1
vote
1
reply
681
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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 2.6 years ago by ★ 27k • written 2.6 years ago by ▴ 90
2
votes
1
reply
1.1k
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QC metrics from pacbio long reads data
coverage QC Long_Reads smrtlink Pacbio
updated 2.6 years ago by ▴ 410 • written 2.6 years ago by ▴ 90
0
votes
0
replies
442
views
How to find adapter dimer present in a library from reads?
adapter_dimer Library
updated 11 months ago by 43k • written 2.7 years ago by ▴ 90
1
vote
2
replies
1.7k
views
converting Bam to fastq while removing clipping(hard/soft clip bases)
Soft-clipping fastq hard-clipping bam
updated 11 months ago by 43k • written 2.7 years ago by ▴ 90
2
votes
4
replies
1.5k
views
Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?
metagenomics_pipelines WGS shotgun_metagenomics antimicrobial_resistance
2.7 years ago by eli_bayat ▴ 90
5
votes
7
replies
1.7k
views
Genomic landscape of Neisseria gonorrhoeae wild-type strain whole genome schematic.
Figures Neisseria_gonorrhoeae regions whole_genome Strain
updated 2.7 years ago by 142k • written 2.7 years ago by ▴ 90
0
votes
0
replies
393
views
Find the copy number of marker genes and the number of them that results in drug resistance?
copy-number 23SrRNA marker-gene drug-Resistance
2.7 years ago by eli_bayat ▴ 90
1
vote
2
replies
823
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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
2.8 years ago by eli_bayat ▴ 90
4
votes
3
replies
1.0k
views
Finding metagenomic short read sequences
antimicrobial reference short sequences reads data metagenomic resistance
updated 2.8 years ago by ★ 1.1k • written 2.8 years ago by ▴ 90
1
vote
2
replies
1.5k
views
identifying strain using pangolin and nextclade
Covid19 pangolin nextstrain strain nextclade
3.1 years ago by eli_bayat ▴ 90
7
votes
4
replies
1.4k
views
SARS-CoV2 strain identifying strain
Covid19 SARS-CoV-2 GISAid
updated 4 months ago by 43k • written 3.1 years ago by ▴ 90
0
votes
5
replies
994
views
blastn --remote option skipping sequences
command-line blast
3.6 years ago by eli_bayat ▴ 90
2
votes
2
replies
866
views
How to get Positive Control gut or Vaginal microbiome dataset
Positive control decontamination filtering
updated 4.2 years ago by 20 • written 4.3 years ago by ▴ 90
1
vote
1
reply
516
views
How to find genes and function of particular species such as Lactobacillus Crispatus?
KEEG Pathway functions bacteria gene
updated 4.3 years ago by 142k • written 4.3 years ago by ▴ 90
3
votes
3
replies
939
views
How to find a pathway from bacteria to disease
gene pathways KEEG disease bacteria
updated 4.3 years ago by ▴ 1000 • written 4.3 years ago by ▴ 90
7
votes
12
replies
7.6k
views
How to Demultiplex a fastq.gz file.
illumina de-multiplexing Miseq fastq dada2
4.7 years ago by eli_bayat ▴ 90
27 results • Page 1 of 1
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