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questions
5
votes
3
replies
348
views
Best genome browser for manual curation of gene structure(s)?
structure
gene
updated 27 days ago by
cmdcolin
★ 3.8k • written 29 days ago by
William
★ 5.3k
3
votes
4
replies
400
views
What can cause broken read-pairs (chimeric read-pairs) in a sequencing run?
QC
3 months ago by
William
★ 5.3k
2
votes
3
replies
439
views
Difference between mRNA and transcript record types in GFF3 and GTF
gff3
updated 3 months ago by
i.sudbery
19k • written 3 months ago by
William
★ 5.3k
4
votes
7
replies
2.9k
views
6 follow
Insillico dual restriction enzyme reference genome digestion.
ddradseq
insillico
updated 6 months ago by
tshtatland
▴ 190 • written 7.8 years ago by
William
★ 5.3k
2
votes
2
replies
2.9k
views
Tools to create flanking sequences for variants based on a VCF file and reference genome.
vcf
assay
updated 7 months ago by
estpallag
▴ 10 • written 7.8 years ago by
William
★ 5.3k
4
votes
12
replies
4.1k
views
6 follow
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 8 months ago by
alejandrogzi
▴ 120 • written 4.0 years ago by
William
★ 5.3k
0
votes
0
replies
283
views
Find reference genome regions spanned by only mapping quality 0 reads in multiple WGS samples
mapping-quality
BAM
FASTA
8 months ago by
William
★ 5.3k
2
votes
1
reply
518
views
Gene prediction in the era of long read sequencing data and many reference genomes
gene-prediction
11 months ago by
William
★ 5.3k
3
votes
3
replies
675
views
Reduce poly-N regions longer than 200bp back to 200bp in a reference genome FASTA
FASTA
poly-N
13 months ago by
William
★ 5.3k
5
votes
2
replies
804
views
How to merge unique/non overlapping genes between 2 gene model GFF3 files?
gff3
updated 15 months ago by
Juke34
8.6k • written 15 months ago by
William
★ 5.3k
1
vote
3
replies
1.0k
views
How to convert VCF (with possible predicted gene effects) to protein fasta/MSA
gff3
fasta
protein
VCF
updated 15 months ago by
Emily
23k • written 15 months ago by
William
★ 5.3k
1
vote
2
replies
810
views
How to estimate and visualize haplotype blocks on a phased VCF/BCF
haplotype
vcf
15 months ago by
William
★ 5.3k
0
votes
1
reply
594
views
Tool that can merge 2 VCF files while taking "representational ambiguity" of (multi-allelic) variants into account
vcf
bcftools
updated 10 months ago by
Ram
43k • written 20 months ago by
William
★ 5.3k
0
votes
0
replies
376
views
How to call SVs between reference genomes and force those SVs to be genotyped in WGS samples?
SVs
21 months ago by
William
★ 5.3k
10
votes
5
replies
7.0k
views
How to determine percentage missing genotypes in VCF/BCF?
vcf
updated 24 months ago by
chrchang523
10k • written 6.9 years ago by
William
★ 5.3k
24
votes
6
replies
10k
views
8 follow
Add contig lenght to VCF header in a robust way
vcf
updated 2.0 years ago by
jena
▴ 290 • written 7.9 years ago by
William
★ 5.3k
6
votes
10
replies
2.7k
views
User friendly (visual&interactive) VCF/BCF mining tools (2021)
gui
vcf
updated 17 months ago by
jena
▴ 290 • written 2.6 years ago by
William
★ 5.3k
0
votes
2
replies
1.3k
views
Best (GATK compatible) RadSeq/GBS pipeline in 2021
radseq
gbs
gatk
updated 2.2 years ago by
rimgubaev
▴ 330 • written 3.2 years ago by
William
★ 5.3k
0
votes
1
reply
2.2k
views
How are features extracted and encoded from a genotype matrix / VCF file?
vcf
statistics
feature extraction
updated 2.2 years ago by
P
▴ 10 • written 7.8 years ago by
William
★ 5.3k
2
votes
1
reply
621
views
How does 23andme store and analyze SNP array data of 12M humans?
snparray
23andme
updated 2.3 years ago by
zx8754
11k • written 2.3 years ago by
William
★ 5.3k
0
votes
0
replies
472
views
Calculate genome regions to exclude for Structural Variant calling
SV
2.5 years ago by
William
★ 5.3k
1
vote
1
reply
816
views
Filter criteria for variants based on GBS data
gbs
filter
updated 2.6 years ago by
Renesh
★ 2.2k • written 2.6 years ago by
William
★ 5.3k
0
votes
2
replies
894
views
Wobbly average GC profile spanning entire R1 read length; what the cause and is it bad
fastq
qc
2.9 years ago by
William
★ 5.3k
3
votes
3
replies
1.3k
views
Best pre and post alignment / variant calling QC tools for many WGS/RNA samples 2021
fastq
vcf
bam
2.9 years ago by
William
★ 5.3k
44
votes
21
replies
34k
views
16 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 15 months ago by
Ram
43k • written 10.6 years ago by
William
★ 5.3k
3
votes
4
replies
3.5k
views
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
2
votes
1
reply
1.2k
views
Convert GFF3 to splice junction BED file, for filtering variants multi-sample (RNA-seq) VCF
rna
splice-junction
vcf
3.1 years ago by
William
★ 5.3k
1
vote
2
replies
2.0k
views
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
4galaxy77
2.8k • written 3.3 years ago by
William
★ 5.3k
2
votes
6
replies
2.9k
views
How to filter a gff3 file by gene IDs
gff3
3.4 years ago by
William
★ 5.3k
4
votes
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
GenoMax
142k • written 3.4 years ago by
William
★ 5.3k
2
votes
2
replies
782
views
Count all (non N) nucleotides within regions defined in BED file
bed
fasta
updated 3.4 years ago by
Prasad
★ 1.6k • written 3.4 years ago by
William
★ 5.3k
0
votes
4
replies
1.5k
views
Best way to find intervals for parallelization of joint variant calling
variants
parallel
updated 3.5 years ago by
Pierre Lindenbaum
161k • written 3.5 years ago by
William
★ 5.3k
3
votes
1
reply
927
views
Split reference genome into callable regions by splitting on NNNN stretches
fasta
bed
updated 3.5 years ago by
Pierre Lindenbaum
161k • written 3.5 years ago by
William
★ 5.3k
9
votes
5
replies
4.6k
views
Best tools for lifting over genome coordinates for non model organism (custom) reference genomes
liftover
updated 3.5 years ago by
Yannick Wurm
★ 2.5k • written 7.4 years ago by
William
★ 5.3k
16
votes
3
replies
9.6k
views
How to export subset of metadata and expression data from BioConductor GEOquery?
R
GEO
bioconductor
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
William
★ 5.3k
1
vote
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
Ram
43k • written 10.9 years ago by
William
★ 5.3k
2
votes
1
reply
1.1k
views
Plotting marker location co-linearity between multiple physical and genetic maps
plotting
ideogram
4.0 years ago by
William
★ 5.3k
0
votes
2
replies
1.5k
views
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
61
votes
14
replies
20k
views
13 follow
Why is Hadoop not used a lot in bio-informatics?
hadoop
updated 14 months ago by
Ram
43k • written 9.6 years ago by
William
★ 5.3k
26
votes
9
replies
20k
views
8 follow
Best Copy Number Variation Tools
cnv
updated 4.5 years ago by
Biostar
20 • written 11.5 years ago by
William
★ 5.3k
0
votes
0
replies
2.9k
views
Best tool to create a graphical (QC) summary report based on a VCF file?
vcf
qc
updated 21 months ago by
Ram
43k • written 8.4 years ago by
William
★ 5.3k
4
votes
7
replies
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
Johan Zicola
▴ 70 • written 10.7 years ago by
William
★ 5.3k
7
votes
6
replies
4.6k
views
Difference between . and ./. for missing genotype in VCF
vcf
updated 2.5 years ago by
Emily
23k • written 5.5 years ago by
William
★ 5.3k
14
votes
3
replies
8.0k
views
Should you decompose and normalize multi-allelic variants for comparison / ID assignment?
multi-allelic
decomposition
normalization
updated 18 months ago by
Ram
43k • written 8.8 years ago by
William
★ 5.3k
4
votes
12
replies
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
Sean Davis
26k • written 6.1 years ago by
William
★ 5.3k
4
votes
11
replies
3.3k
views
Sensitive (BLAST like) and fast alignment of millions of sequences against human sized reference genomes
blast
bwa
alignment
lift over
multicopy
updated 6.3 years ago by
lieven.sterck
15k • written 6.3 years ago by
William
★ 5.3k
5
votes
4
replies
2.2k
views
Should I use a bad/ mediocre gene model as input for STAR RNA-seq alignment?
RNA-Seq
star
gene_model
incremental
updated 6.3 years ago by
Santosh Anand
5.7k • written 6.3 years ago by
William
★ 5.3k
3
votes
6
replies
2.7k
views
How to display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)?
vcf
gui
updated 5 months ago by
Jeremy Leipzig
22k • written 6.6 years ago by
William
★ 5.3k
0
votes
3
replies
1.4k
views
How to do a local denovo assembly including unmapped paired reads for many samples to genotype a large insertion.
local assembly
updated 6.7 years ago by
h.mon
35k • written 6.7 years ago by
William
★ 5.3k
2
votes
3
replies
2.3k
views
Is it possible to use haplotypes instead of SNPs for association testing with phenotypes?
SNP
haplotypes
gwas
updated 6.8 years ago by
GabrielMontenegro
▴ 670 • written 6.8 years ago by
William
★ 5.3k
139 results • Page
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