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Comment: Comment: 2021: state and usuge of compressed file standards better than BAM and FASTQ
3.0 years ago by William ★ 5.3k
0
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1
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3.4k
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Comment: Comment: 2021: state and usuge of compressed file standards better than BAM and FASTQ
3.0 years ago by William ★ 5.3k
3
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4
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3.5k
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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
2.7 years ago by William ★ 5.3k
1
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1
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3.5k
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Answer: Answer: How to set variant FILTER in a VCF file based on overlap with regions in a BED
3.0 years ago by William ★ 5.3k
2
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1
reply
1.2k
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Convert GFF3 to splice junction BED file, for filtering variants multi-sample (RNA-seq) VCF
rna splice-junction vcf
3.0 years ago by William ★ 5.3k
1
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0
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1.2k
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Answer: Answer: Convert GFF3 to splice junction BED file, for filtering variants multi-sample (
3.0 years ago by William ★ 5.3k
0
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0
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1.3k
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Comment: C: Best (GATK compatible) RadSeq/GBS pipeline in 2021
3.1 years ago by William ★ 5.3k
0
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0
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2.0k
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Comment: C: How to convert a VCF with genotypes and phasing info to list of haplotypes for R
3.3 years ago by William ★ 5.3k
1
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2
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2.0k
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How to convert a VCF with genotypes and phasing info to list of haplotypes for ROI/SOI
vcf genotypes phasing haplotypes
updated 3.3 years ago by 2.8k • written 3.3 years ago by ★ 5.3k
1
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0
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2.9k
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Comment: C: How to filter a gff3 file by gene IDs
3.3 years ago by William ★ 5.3k
0
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0
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2.9k
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Comment: C: How to filter a gff3 file by gene IDs
3.3 years ago by William ★ 5.3k
0
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1
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2.9k
views
Comment: C: How to filter a gff3 file by gene IDs
3.3 years ago by William ★ 5.3k
2
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6
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2.9k
views
How to filter a gff3 file by gene IDs
gff3
3.3 years ago by William ★ 5.3k
4
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2
replies
2.1k
views
How to "discover" read structure and barcodes given Illumina sequencing run directory
bcl illumina barcodes demultiplexing
updated 3.4 years ago by 141k • written 3.4 years ago by ★ 5.3k
1
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0
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2.1k
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Answer: A: How to "discover" read structure and barcodes given Illumina sequencing run dire
3.4 years ago by William ★ 5.3k
0
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0
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776
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Comment: C: Count all (non N) nucleotides within regions defined in BED file
3.4 years ago by William ★ 5.3k
0
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0
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10k
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Answer: A: Counting base and nucleotide frequency of multifasta file
3.4 years ago by William ★ 5.3k
2
votes
2
replies
776
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Count all (non N) nucleotides within regions defined in BED file
bed fasta
updated 3.4 years ago by ★ 1.6k • written 3.4 years ago by ★ 5.3k
0
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0
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1.5k
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Comment: C: Best way to find intervals for parallelization of joint variant calling
3.4 years ago by William ★ 5.3k
0
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1
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1.5k
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Comment: C: Best way to find intervals for parallelization of joint variant calling
3.4 years ago by William ★ 5.3k
0
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4
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1.5k
views
Best way to find intervals for parallelization of joint variant calling
variants parallel
updated 3.4 years ago by 161k • written 3.4 years ago by ★ 5.3k
3
votes
1
reply
925
views
Split reference genome into callable regions by splitting on NNNN stretches
fasta bed
updated 3.4 years ago by 161k • written 3.4 years ago by ★ 5.3k
9
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5
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4.6k
views
Best tools for lifting over genome coordinates for non model organism (custom) reference genomes
liftover
updated 3.5 years ago by ★ 2.5k • written 7.4 years ago by ★ 5.3k
16
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3
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9.6k
views
How to export subset of metadata and expression data from BioConductor GEOquery?
R GEO bioconductor
updated 2.3 years ago by 43k • written 9.6 years ago by ★ 5.3k
1
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2
replies
5.1k
views
How To Adjust Bwa Mem To Allow For Longer Gaps In Contig Alignment
bwa-mem
updated 19 months ago by 43k • written 10.9 years ago by ★ 5.3k
2
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1
reply
1.1k
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Plotting marker location co-linearity between multiple physical and genetic maps
plotting ideogram
3.9 years ago by William ★ 5.3k
2
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0
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1.1k
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Answer: A: Plotting marker location co-linearity between multiple physical and genetic maps
3.9 years ago by William ★ 5.3k
0
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2
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4.1k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
4.0 years ago by William ★ 5.3k
0
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1
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4.1k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
4.0 years ago by William ★ 5.3k
0
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1
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4.1k
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Comment: C: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
4.0 years ago by William ★ 5.3k
0
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2
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1.5k
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How to remove duplicate reads / create consensus reads based on umi tags in 2nd fastq file?
umi
4.3 years ago by William ★ 5.3k
16
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3
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34k
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Answer: A: Multi-Sample Vcf To Phylogenetic Tree.
updated 4.4 years ago by 43k • written 10.5 years ago by ★ 5.3k
61
votes
14
replies
20k
views
13 follow
Why is Hadoop not used a lot in bio-informatics?
hadoop
updated 13 months ago by 43k • written 9.6 years ago by ★ 5.3k
4
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0
replies
6.2k
views
Answer: A: Do freeBayes and platypus support gVCF (ie incremental variant calling for large
updated 4.4 years ago by 43k • written 8.5 years ago by ★ 5.3k
26
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9
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20k
views
8 follow
Best Copy Number Variation Tools
cnv
updated 4.4 years ago by 20 • written 11.5 years ago by ★ 5.3k
2
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0
replies
3.7k
views
Answer: A: Ideal practice to manage huge NGS dataset/Intermediate files of Whole Genome Hum
updated 4.5 years ago by 43k • written 8.6 years ago by ★ 5.3k
0
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0
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2.9k
views
Best tool to create a graphical (QC) summary report based on a VCF file?
vcf qc
updated 20 months ago by 43k • written 8.4 years ago by ★ 5.3k
1
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2
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20k
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Answer: A: Why is Hadoop not used a lot in bio-informatics?
updated 4.5 years ago by 43k • written 9.5 years ago by ★ 5.3k
0
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0
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3.7k
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Answer: A: Breakdancer Compile Error: Regionlimitedbamreader.Hpp:23:5: Error: ‘Bam_Iter_T’
updated 4.6 years ago by 43k • written 10.7 years ago by ★ 5.3k
0
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1
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3.7k
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Comment: C: Breakdancer Compile Error: Regionlimitedbamreader.Hpp:23:5: Error: ‘Bam_Iter_T’
updated 4.6 years ago by 43k • written 10.7 years ago by ★ 5.3k
1
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0
replies
17k
views
Comment: C: Combine Single Sample Vcf To Multi Sample Vcf
updated 5.3 years ago by 43k • written 10.9 years ago by ★ 5.3k
7
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1
reply
39k
views
Answer: A: Combining Data Of Multiple Vcfs Into One.
updated 5.3 years ago by 11k • written 10.9 years ago by ★ 5.3k
4
votes
7
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6.4k
views
How To Find The Locations Of A Short Specific Sequence In A Genome With 1 Or 2 Mismatches Allowed?
bwa blast sequence
updated 5.3 years ago by ▴ 70 • written 10.7 years ago by ★ 5.3k
0
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0
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4.6k
views
Comment: C: Difference between . and ./. for missing genotype in VCF
5.4 years ago by William ★ 5.3k
7
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6
replies
4.6k
views
Difference between . and ./. for missing genotype in VCF
vcf
updated 2.5 years ago by 23k • written 5.4 years ago by ★ 5.3k
14
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3
replies
8.0k
views
Should you decompose and normalize multi-allelic variants for comparison / ID assignment?
multi-allelic decomposition normalization
updated 17 months ago by 43k • written 8.8 years ago by ★ 5.3k
0
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1
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4.2k
views
Answer: A: find homozygous SNPs between two samples's VCF files.
6.1 years ago by William ★ 5.3k
4
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12
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3.3k
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 6.1 years ago by 26k • written 6.1 years ago by ★ 5.3k
0
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0
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3.3k
views
Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
6.1 years ago by William ★ 5.3k
0
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0
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3.3k
views
Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
6.1 years ago by William ★ 5.3k
385 results • Page 2 of 8
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