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VCF filtering settings for WES
vcf next-gen wes vcf filtering filtering written 22 hours ago by luca t • 0
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3.9k
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5 follow
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Tool: fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
qc fastp filtering tool written 2.5 years ago by chen • 2.1k • updated 8 days ago by leonardo.rippel • 20
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135
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Filter max-missing multiple time removes more SNPs
linux vcftools snp filtering sequencing written 4 weeks ago by QPaps04 • 20
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172
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Filtering bacterial genes by annotations and finding common genes between genomes
cordon codon usage bias annotations filtering written 3 months ago by dch014 • 0 • updated 8 weeks ago by Biostar ♦♦ 20
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677
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1
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Filtering for Percentage of identity (sequence identity: pident, %) from tblastn results
sequence pident blast filtering tblastn written 19 months ago by endretoth • 20
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Filtering lowly expressed genes - edgeR
R filtering rna-seq edger written 3.0 years ago by noeD • 90 • updated 3 months ago by CL • 0
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3
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542
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3
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GATK VariantFiltration does not filter [SOLVED]
genome gatk variantfiltration filtering snp written 4 months ago by romain.coppee • 0
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1
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324
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5 follow
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filtered tab delimited file with awk
assembly text filtering file written 5 months ago by yaghoub.amraei • 10 • updated 5 months ago by Pierre Lindenbaum ♦ 133k
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424
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Highly biased experiment showing funny histogram of p values for all tests. Suggestions?
deseq2 rna-seq filtering written 17 months ago by Mozart • 240
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150
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Evaluating RMSMappingQuality profile to set threshold
variant calling gatk snp filtering written 7 months ago by serpalma.v • 60 • updated 7 months ago by Nicolas Rosewick ♦ 9.3k
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185
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How can I filter RNA-seq reads to remove reads where more than 50% of the read is low quality (Q<20)?
genome quality rna-seq filtering written 8 months ago by mar77 • 20
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How to filter out mouse cells to from a mixture library (mouse and human cells) by cellranger?
mix library scrna filtering written 2.1 years ago by mzhoufulai • 0 • updated 8 months ago by swbarnes2 ♦ 9.4k
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352
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ReadPosRankSum annotation error (gatk4)
gatk variants readposranksum filtering vqsr written 8 months ago by Cricket • 10
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341
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Structural variant filtering
structural variant filtering written 8 months ago by dominique.massau • 0
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424
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filtering unmapped and multiple mapped reads
smatools filtering rna-seq written 9 months ago by annaA • 10
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349
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What causes strange oscillations in the count distribution of Salmon and STAR aligned gene tables?
htseq salmon star filtering counts written 9 months ago by Gabriel • 90
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297
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How to add a flag to a sam/bam file
flag samtools atac-seq filtering written 11 months ago by nanoide • 60 • updated 9 months ago by Biostar ♦♦ 20
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260
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How to get Positive Control gut or Vaginal microbiome dataset
positive control decontamination filtering written 12 months ago by eli_bayat • 20 • updated 10 months ago by Biostar ♦♦ 20
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1
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379
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1
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How to create a bed file from a fasta containing all regions with clusters of >= 50 Ns and flanking 1kb regions
genome bed filtering fasta written 10 months ago by Rubal • 330 • updated 10 months ago by ATpoint ♦ 44k
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387
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ADMIXTURE optimal k depends on filters?
snp admixture plink filtering cross-validation written 11 months ago by RvV • 0
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183
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Application of empty blast result
blast filtering empty written 11 months ago by marongiu.luigi • 520
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305
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1
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Understanding variants that PASS filter but are also flagged?
filtering written 12 months ago by rthomas • 10
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201
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Eliminating panel mutations based on coverage of PoN
gatk filtering written 12 months ago by vctrm67 • 20
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604
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Where to set intensity filtering threshold if oligo::rma returns large peak of very low intensities for Affymetrix microarrays?
microarray filtering limma written 18 months ago by Mari • 0 • updated 13 months ago by Biostar ♦♦ 20
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gatk SelectVariants odd behavior
selectvariants gatk vcf filtering snp written 21 months ago by jon.klonowski • 70 • updated 13 months ago by cricgpu • 0
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1
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314
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1
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Low mean of read depth - filtering SNP in VCF file
vcf snp filtering written 14 months ago by Trevorsky • 0 • updated 14 months ago by joneill4x • 110
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1
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619
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1
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Filtering for individual allelic balance in multisample vcf using GATK4
vcf gatk gatk4 filtering written 15 months ago by mernster • 0 • updated 15 months ago by chrchang523 ♦ 7.6k
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1
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377
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1
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Not enough SNPs after filtering an imputed dataset
snp impute filtering qctool variants written 15 months ago by Max • 20
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628
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Error: Bad BCF record - shared section malformed or too short after vcftools filtering
vcf bcf filtering snp written 15 months ago by yvanpapa • 0
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Code to select randomly 1 SNP per scaffold
vcf snp filtering random selection written 2.7 years ago by angelaparody • 80 • updated 15 months ago by Biostar ♦♦ 20
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