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questions
0
votes
0
replies
181
views
Advice on telling if two SNPs are on the same haplotype
ldpair
halplotype
co-occurance
gnomad
snp
10 weeks ago by
amy__
▴ 160
0
votes
13
replies
977
views
Help with the new nomenclature of multi-nucleotide variants
bam
igv
multinucleotide
11 weeks ago by
amy__
▴ 160
2
votes
4
replies
646
views
If the mane transcript isn't available should you use the canonical transcript?
ensembl
mane
gnomad
canonical
11 weeks ago by
amy__
▴ 160
0
votes
1
reply
314
views
LOFTEE flag on GnomAD - END_TRUNC
loftee
gnomad
updated 3 months ago by
Pierre Lindenbaum
162k • written 3 months ago by
amy__
▴ 160
0
votes
1
reply
239
views
Extracting LOF variants and incidence from GnomAD for a list of genes
Gnomad
LOF
genes
updated 4 months ago by
LauferVA
4.2k • written 4 months ago by
amy__
▴ 160
2
votes
6
replies
886
views
Genotypes in vcf files
genotypes
vcf
updated 6 months ago by
Jeremy Leipzig
22k • written 6 months ago by
amy__
▴ 160
0
votes
0
replies
324
views
Filtering vcf by strand bias / annotating strand bias on
Vcf
updated 7 months ago by
Ram
44k • written 7 months ago by
amy__
▴ 160
0
votes
1
reply
397
views
How to find the most representative protein data base ID for your protein?
modelling
protein
database
updated 8 months ago by
GenoMax
142k • written 8 months ago by
amy__
▴ 160
1
vote
3
replies
544
views
Classification for low quality variant on IGV
bam
igv
updated 10 months ago by
dthorbur
★ 2.0k • written 10 months ago by
amy__
▴ 160
6
votes
2
replies
912
views
IGV - is it possible to tell what allele a read is from?
WES
reads
IGV
10 months ago by
amy__
▴ 160
1
vote
2
replies
520
views
Low coverage in specific exons of genes - sequencing errors?
coverage
10 months ago by
amy__
▴ 160
0
votes
4
replies
882
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
11 months ago by
amy__
▴ 160
0
votes
0
replies
356
views
GC content of WES cohort
WES
FASTQC
GC-content
updated 12 months ago by
Ram
44k • written 12 months ago by
amy__
▴ 160
1
vote
1
reply
495
views
Variant depth cut off - justification
VCF
depth
variant
updated 13 months ago by
dthorbur
★ 2.0k • written 13 months ago by
amy__
▴ 160
4
votes
3
replies
702
views
Is it possible to do bedtools multicov across the entire genome?
bedtools
updated 11 months ago by
Ram
44k • written 15 months ago by
amy__
▴ 160
0
votes
0
replies
332
views
Haloplex HS - should you remove duplicates?
deduplicate
Haloplex
duplicates
16 months ago by
amy__
▴ 160
3
votes
3
replies
767
views
liftover output column help
liftover
updated 16 months ago by
Pierre Lindenbaum
162k • written 16 months ago by
amy__
▴ 160
0
votes
0
replies
298
views
GQ score - what do the numbers mean? How can this be interpreted?
vcf
GQ
19 months ago by
amy__
▴ 160
0
votes
3
replies
586
views
Add absolute colours to heat map depending on range
heatmap
pheatmap
updated 19 months ago by
Matthias Zepper
4.6k • written 19 months ago by
amy__
▴ 160
3
votes
3
replies
1.8k
views
bcftools split-vep -- how to split the INFO column up and also assign the ensembl vep headers
bcftools
ensembl-vep
vep
updated 11 months ago by
Ram
44k • written 20 months ago by
amy__
▴ 160
0
votes
6
replies
1.3k
views
Missing reads in fastp
fastp
filtering
trimming
updated 21 months ago by
Istvan Albert
100k • written 22 months ago by
amy__
▴ 160
14
votes
12
replies
4.5k
views
6 follow
Which hg38 file?
reference
hg38
NCBI
updated 9 months ago by
ATpoint
82k • written 22 months ago by
amy__
▴ 160
0
votes
15
replies
2.2k
views
Chromosome accession numbers correspond to which chromosome?
bam
chromosome
bed
19 months ago by
amy__
▴ 160
1
vote
2
replies
2.6k
views
fastp ERROR: igzip: encountered while decompressing file:
fastp
igzip
trimming
updated 22 months ago by
GenoMax
142k • written 22 months ago by
amy__
▴ 160
3
votes
5
replies
1.9k
views
qualimap - bed file error - BED format error, there should be at least 6 fields.
qualimap
updated 24 months ago by
Alex Reynolds
35k • written 24 months ago by
amy__
▴ 160
2
votes
3
replies
1.4k
views
bedcov output meaning
coverage
read
bedcov
updated 24 months ago by
Pierre Lindenbaum
162k • written 24 months ago by
amy__
▴ 160
7
votes
9
replies
1.5k
views
Do you need to define adapter sequences for trimming and QC tools?
adapters
fastp
illumina
trimming
2.0 years ago by
amy__
▴ 160
2
votes
2
replies
565
views
Single-read mapped reads? Fastp paper unclear
fastp
single-read
reads
2.1 years ago by
amy__
▴ 160
9
votes
7
replies
1.7k
views
How to work out coverage (100X) of WES using exome bed file?
bed
WES
coverage
updated 14 months ago by
Ram
44k • written 2.1 years ago by
amy__
▴ 160
4
votes
3
replies
3.0k
views
Errors when using samtools faidx and bgzip for indexing human reference genome
bgzip
samtools
updated 11 months ago by
Ram
44k • written 2.2 years ago by
amy__
▴ 160
1
vote
1
reply
587
views
Copy of FASTQC documentation pdf
fastqc
documentation
updated 2.2 years ago by
Istvan Albert
100k • written 2.2 years ago by
amy__
▴ 160
0
votes
7
replies
1.4k
views
How to make a diagram of a gene?
gene
diagram
updated 2.3 years ago by
Dunois
★ 2.5k • written 2.3 years ago by
amy__
▴ 160
0
votes
2
replies
642
views
bwa index - failed to find .pac
index
.pac
hpc
bwa
2.3 years ago by
amy__
▴ 160
1
vote
1
reply
781
views
Input and output of picard markduplicate for deepvariant
markduplicates
picard
bam
sam
deepvariant
updated 2.4 years ago by
jv
★ 1.8k • written 2.4 years ago by
amy__
▴ 160
0
votes
2
replies
687
views
Should your variant calling pipeline change depending on whether using WES or WGS?
calling
WGS
WES
Variant
2.6 years ago by
amy__
▴ 160
0
votes
3
replies
939
views
strange looking bcftools norm file
bcftools
samtools
variant
updated 11 months ago by
Ram
44k • written 3.2 years ago by
amy__
▴ 160
0
votes
7
replies
1.1k
views
subread keeps makes a weird .sam file, have i done something wrong?
subread
rsubread
alignment
DNA
reference
3.3 years ago by
amy__
▴ 160
37 results • Page
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