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Comment: Comment: 2021: state and usuge of compressed file standards better than BAM and FASTQ
4.4 years ago by William ★ 5.4k
0
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1
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5.0k
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Comment: Comment: 2021: state and usuge of compressed file standards better than BAM and FASTQ
4.4 years ago by William ★ 5.4k
0
votes
1
reply
5.0k
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Comment: Comment: 2021: state and usuge of compressed file standards better than BAM and FASTQ
4.4 years ago by William ★ 5.4k
3
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4
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4.7k
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How to set variant FILTER in a VCF file based on overlap with regions in a BED file
annotation bed vcf
4.1 years ago by William ★ 5.4k
1
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1
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4.7k
views
Answer: Answer: How to set variant FILTER in a VCF file based on overlap with regions in a BED
4.4 years ago by William ★ 5.4k
2
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1
reply
1.6k
views
Convert GFF3 to splice junction BED file, for filtering variants multi-sample (RNA-seq) VCF
rna splice-junction vcf
4.4 years ago by William ★ 5.4k
1
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0
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1.6k
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Answer: Answer: Convert GFF3 to splice junction BED file, for filtering variants multi-sample (
4.4 years ago by William ★ 5.4k
0
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0
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2.0k
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Comment: C: Best (GATK compatible) RadSeq/GBS pipeline in 2021
4.5 years ago by William ★ 5.4k
0
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0
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2.7k
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Comment: C: How to convert a VCF with genotypes and phasing info to list of haplotypes for R
4.7 years ago by William ★ 5.4k
1
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2
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2.7k
views
How to convert a VCF with genotypes and phasing info to list of haplotypes for ROI/SOI
vcf genotypes phasing haplotypes
updated 4.7 years ago by 2.9k • written 4.7 years ago by ★ 5.4k
1
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0
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3.8k
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Comment: C: How to filter a gff3 file by gene IDs
4.7 years ago by William ★ 5.4k
0
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0
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3.8k
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Comment: C: How to filter a gff3 file by gene IDs
4.7 years ago by William ★ 5.4k
0
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1
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3.8k
views
Comment: C: How to filter a gff3 file by gene IDs
4.7 years ago by William ★ 5.4k
2
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6
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3.8k
views
How to filter a gff3 file by gene IDs
gff3
4.7 years ago by William ★ 5.4k
4
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2
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2.6k
views
How to "discover" read structure and barcodes given Illumina sequencing run directory
bcl illumina barcodes demultiplexing
updated 4.7 years ago by 153k • written 4.7 years ago by ★ 5.4k
1
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0
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2.6k
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Answer: A: How to "discover" read structure and barcodes given Illumina sequencing run dire
4.7 years ago by William ★ 5.4k
0
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0
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1.1k
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Comment: C: Count all (non N) nucleotides within regions defined in BED file
4.8 years ago by William ★ 5.4k
0
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0
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11k
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Answer: A: Counting base and nucleotide frequency of multifasta file
4.8 years ago by William ★ 5.4k
2
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2
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1.1k
views
Count all (non N) nucleotides within regions defined in BED file
bed fasta
updated 4.8 years ago by ★ 1.6k • written 4.8 years ago by ★ 5.4k
0
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0
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2.0k
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Comment: C: Best way to find intervals for parallelization of joint variant calling
4.8 years ago by William ★ 5.4k
0
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1
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2.0k
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Comment: C: Best way to find intervals for parallelization of joint variant calling
4.8 years ago by William ★ 5.4k
2
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4
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2.0k
views
Best way to find intervals for parallelization of joint variant calling
variants parallel
updated 4.8 years ago by 166k • written 4.8 years ago by ★ 5.4k
3
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1
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1.2k
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Split reference genome into callable regions by splitting on NNNN stretches
fasta bed
updated 4.8 years ago by 166k • written 4.8 years ago by ★ 5.4k
10
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5
replies
5.6k
views
Best tools for lifting over genome coordinates for non model organism (custom) reference genomes
liftover
updated 4.9 years ago by ★ 2.5k • written 8.8 years ago by ★ 5.4k
16
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3
replies
10k
views
How to export subset of metadata and expression data from BioConductor GEOquery?
R GEO bioconductor
updated 3.7 years ago by 45k • written 11.0 years ago by ★ 5.4k
1
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2
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5.6k
views
How To Adjust Bwa Mem To Allow For Longer Gaps In Contig Alignment
bwa-mem
updated 3.0 years ago by 45k • written 12.2 years ago by ★ 5.4k
2
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1
reply
1.4k
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Plotting marker location co-linearity between multiple physical and genetic maps
plotting ideogram
5.3 years ago by William ★ 5.4k
2
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0
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1.4k
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Answer: A: Plotting marker location co-linearity between multiple physical and genetic maps
5.3 years ago by William ★ 5.4k
0
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2
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5.8k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
5.3 years ago by William ★ 5.4k
0
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1
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5.8k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
5.3 years ago by William ★ 5.4k
0
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1
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5.8k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
5.4 years ago by William ★ 5.4k
0
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2
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1.8k
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How to remove duplicate reads / create consensus reads based on umi tags in 2nd fastq file?
umi
5.7 years ago by William ★ 5.4k
16
votes
3
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39k
views
Answer: A: Multi-Sample Vcf To Phylogenetic Tree.
updated 5.8 years ago by 45k • written 11.9 years ago by ★ 5.4k
61
votes
14
replies
21k
views
13 follow
Why is Hadoop not used a lot in bio-informatics?
hadoop
updated 2.5 years ago by 45k • written 10.9 years ago by ★ 5.4k
4
votes
0
replies
6.7k
views
Answer: A: Do freeBayes and platypus support gVCF (ie incremental variant calling for large
updated 5.8 years ago by 45k • written 9.8 years ago by ★ 5.4k
26
votes
9
replies
21k
views
8 follow
Best Copy Number Variation Tools
cnv
updated 5.8 years ago by 20 • written 12.8 years ago by ★ 5.4k
2
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0
replies
4.5k
views
Answer: A: Ideal practice to manage huge NGS dataset/Intermediate files of Whole Genome Hum
updated 5.8 years ago by 45k • written 9.9 years ago by ★ 5.4k
0
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0
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3.2k
views
Best tool to create a graphical (QC) summary report based on a VCF file?
vcf qc
updated 3.1 years ago by 45k • written 9.8 years ago by ★ 5.4k
1
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2
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21k
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Answer: A: Why is Hadoop not used a lot in bio-informatics?
updated 5.9 years ago by 45k • written 10.9 years ago by ★ 5.4k
0
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0
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4.1k
views
Answer: A: Breakdancer Compile Error: Regionlimitedbamreader.Hpp:23:5: Error: ‘Bam_Iter_T’
updated 5.9 years ago by 45k • written 12.1 years ago by ★ 5.4k
0
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1
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4.1k
views
Comment: C: Breakdancer Compile Error: Regionlimitedbamreader.Hpp:23:5: Error: ‘Bam_Iter_T’
updated 5.9 years ago by 45k • written 12.1 years ago by ★ 5.4k
1
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0
replies
18k
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Comment: C: Combine Single Sample Vcf To Multi Sample Vcf
updated 6.6 years ago by 45k • written 12.3 years ago by ★ 5.4k
7
votes
1
reply
41k
views
Answer: A: Combining Data Of Multiple Vcfs Into One.
updated 6.7 years ago by 12k • written 12.3 years ago by ★ 5.4k
4
votes
7
replies
7.2k
views
How To Find The Locations Of A Short Specific Sequence In A Genome With 1 Or 2 Mismatches Allowed?
bwa blast sequence
updated 6.7 years ago by ▴ 80 • written 12.1 years ago by ★ 5.4k
0
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0
replies
5.6k
views
Comment: C: Difference between . and ./. for missing genotype in VCF
6.8 years ago by William ★ 5.4k
7
votes
6
replies
5.6k
views
Difference between . and ./. for missing genotype in VCF
vcf
updated 3.9 years ago by 24k • written 6.8 years ago by ★ 5.4k
15
votes
3
replies
9.8k
views
Should you decompose and normalize multi-allelic variants for comparison / ID assignment?
multi-allelic decomposition normalization
updated 2.8 years ago by 45k • written 10.2 years ago by ★ 5.4k
0
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1
reply
5.3k
views
Answer: A: find homozygous SNPs between two samples's VCF files.
7.5 years ago by William ★ 5.4k
4
votes
12
replies
4.1k
views
How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using BCFTools,CYVCF2 or Excel
R VCF SNP filtering
updated 7.5 years ago by 27k • written 7.5 years ago by ★ 5.4k
0
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0
replies
4.1k
views
Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
7.5 years ago by William ★ 5.4k
385 results • Page 2 of 8
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