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Showing :
questions
3
votes
6
replies
3.7k
views
Remove both pair end reads with low mapping quality using Samtools
mapping-quality
samtools
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
DVA
▴ 630
1
vote
0
replies
1.4k
views
Get Pseudotime Matrix in Monocole2?
monocole2
4.5 years ago by
DVA
▴ 630
2
votes
2
replies
975
views
Check Conservation of a Given Protein Domain
blast
updated 5.1 years ago by
Bill Pearson
★ 1.0k • written 5.1 years ago by
DVA
▴ 630
4
votes
3
replies
1.3k
views
What happens when SNV caller looks at a SV (e.g. deletion) region?
snv
deletion
updated 5.1 years ago by
WouterDeCoster
47k • written 5.1 years ago by
DVA
▴ 630
0
votes
1
reply
1.0k
views
RNA Expression Pathway Database
database
updated 5.2 years ago by
Biostar
20 • written 5.4 years ago by
DVA
▴ 630
0
votes
2
replies
1.3k
views
Differential Binding in Partek
ChIP-Seq
ATAC-seq
Partek
updated 5.2 years ago by
kgosche
▴ 30 • written 5.2 years ago by
DVA
▴ 630
1
vote
2
replies
1.0k
views
How to handle RNASeq reads that can map to both human and mouse ref (e.g. conserved gene regions)?
alignment
hisat2
updated 5.4 years ago by
JC
13k • written 5.4 years ago by
DVA
▴ 630
0
votes
2
replies
1.9k
views
CIGAR and sequence length are inconsistent after HISAT alignment
hisat
alignment
rnaseq
updated 5.5 years ago by
Devon Ryan
104k • written 5.5 years ago by
DVA
▴ 630
4
votes
6
replies
1.2k
views
Count 0, 5, 20 covered sites in bam
wgs
bam
updated 5.6 years ago by
Pierre Lindenbaum
161k • written 5.6 years ago by
DVA
▴ 630
1
vote
2
replies
1.0k
views
Extract the overlap of well-covered regions across multiple samples
coverage
WGS
5.8 years ago by
DVA
▴ 630
3
votes
2
replies
1.7k
views
Pathway enrichment with differential expression p-values
gene enrichment
updated 5.8 years ago by
Benn
8.3k • written 5.8 years ago by
DVA
▴ 630
1
vote
1
reply
1.2k
views
GSEA Phenotype Table Input
gsea
updated 5.8 years ago by
c.chakraborty
▴ 170 • written 5.9 years ago by
DVA
▴ 630
0
votes
0
replies
1.8k
views
Multiple factors & batch effects - DESeq2
deseq2
5.9 years ago by
DVA
▴ 630
2
votes
3
replies
3.4k
views
Horizontal lines in MA plot (DESeq2)
deseq2
5.9 years ago by
DVA
▴ 630
4
votes
10
replies
4.4k
views
Which annotation file to use
RNA-Seq
updated 6.0 years ago by
h.mon
35k • written 6.0 years ago by
DVA
▴ 630
4
votes
4
replies
6.3k
views
High Unassigned Ambiguity in Feature Counts
feature count
updated 6.0 years ago by
michael.ante
★ 3.8k • written 6.0 years ago by
DVA
▴ 630
3
votes
6
replies
2.0k
views
Mask gtf file for cufflinks
RNA-Seq
6.0 years ago by
DVA
▴ 630
8
votes
2
replies
2.4k
views
HISAT2 tmo and rna-strandness options not working as expected
RNA-Seq
6.1 years ago by
DVA
▴ 630
0
votes
3
replies
2.2k
views
Reasons for polyA in RNA Seq Reads
RNA-Seq
6.1 years ago by
DVA
▴ 630
4
votes
2
replies
2.2k
views
Base pair order in sequencer vs in fastq
sequencing
updated 6.1 years ago by
finswimmer
16k • written 6.1 years ago by
DVA
▴ 630
10
votes
13
replies
5.3k
views
Best way to trim PolyA in RNA Seq reads?
RNA-Seq
updated 6.1 years ago by
WouterDeCoster
47k • written 6.1 years ago by
DVA
▴ 630
5
votes
10
replies
4.2k
views
High A in "Per base sequence content" of fastQC report
fastqc
6.1 years ago by
DVA
▴ 630
2
votes
9
replies
2.1k
views
Analysis of sequencing duplicates
duplicate
updated 6.4 years ago by
GenoMax
141k • written 6.4 years ago by
DVA
▴ 630
0
votes
0
replies
1.1k
views
Locate LOH using SNV VCF files
snp
6.4 years ago by
DVA
▴ 630
3
votes
4
replies
2.2k
views
Locate positions in a large bed file
bed
updated 6.5 years ago by
Alex Reynolds
35k • written 6.5 years ago by
DVA
▴ 630
3
votes
5
replies
3.8k
views
Mutect 2 on WGS data takes too long to run
mutect
wgs
updated 6.7 years ago by
donfreed
★ 1.6k • written 6.7 years ago by
DVA
▴ 630
6
votes
3
replies
2.5k
views
somatic calls by somatic SNV caller differ a lot, when comparing with cancer minors normal germline calls
somatic
SNV
SNP
updated 6.7 years ago by
d-cameron
★ 2.9k • written 6.7 years ago by
DVA
▴ 630
3
votes
3
replies
2.4k
views
GT field in VCF only has one number?
vcf
6.7 years ago by
DVA
▴ 630
2
votes
2
replies
2.2k
views
Effectively search for positions in large bedgraph files using python (or other language if needed)
bedgraph
python
updated 6.8 years ago by
Alex Reynolds
35k • written 6.8 years ago by
DVA
▴ 630
3
votes
2
replies
2.3k
views
snpEff database to annotate b37 GATK output
snpeff
gatk
updated 6.8 years ago by
hns
▴ 150 • written 7.0 years ago by
DVA
▴ 630
4
votes
5
replies
4.1k
views
No output from samtools index?
samtools
6.9 years ago by
DVA
▴ 630
50
votes
17
replies
5.5k
views
7 follow
Develop an R package for CRAN vs BioConductor
bioconductor
cran
r
packages
updated 7.2 years ago by
ddiez
★ 2.0k • written 7.2 years ago by
DVA
▴ 630
10
votes
11
replies
7.5k
views
Extract surrounding genome sequences given certain locations using R
R
package
genome
sequence
updated 7.3 years ago by
ddiez
★ 2.0k • written 7.3 years ago by
DVA
▴ 630
3
votes
2
replies
1.5k
views
Convert BLAST NC_ labels to chromosome label
blast
updated 7.3 years ago by
mastal511
★ 2.1k • written 7.3 years ago by
DVA
▴ 630
0
votes
1
reply
1.2k
views
Other genetic variants representation format besides VCF
vcf
variants
updated 7.3 years ago by
Brian Bushnell
20k • written 7.3 years ago by
DVA
▴ 630
10
votes
10
replies
9.7k
views
How do people know to use at least 30X coverage in WGS?
sequencing
wgs
coverage
updated 7.4 years ago by
Brian Bushnell
20k • written 7.5 years ago by
DVA
▴ 630
2
votes
2
replies
2.8k
views
Large input when using jellyfish
jellyfish
next-gen
whole genome seq
7.5 years ago by
DVA
▴ 630
10
votes
8
replies
3.3k
views
Non-cancer somatic mutation calling
somatic mutations
mutect
varscan
samtools
gatk
7.9 years ago by
DVA
▴ 630
1
vote
1
reply
2.3k
views
VCFtools: how does --diff option consider genotypes
vcf
updated 21 months ago by
Ram
43k • written 8.2 years ago by
DVA
▴ 630
0
votes
0
replies
3.6k
views
Output all allele counts at each position using bcftools
bcftools
samtools
8.1 years ago by
DVA
▴ 630
2
votes
2
replies
1.6k
views
Extract genotype from hg19
hg19
updated 8.2 years ago by
Chris Fields
★ 2.2k • written 8.2 years ago by
DVA
▴ 630
3
votes
5
replies
2.0k
views
Can't locate dbSNP 131 anymore?
dbsnp
updated 21 months ago by
Ram
43k • written 8.2 years ago by
DVA
▴ 630
0
votes
1
reply
1.3k
views
Microarray vs WGS using a real dataset?
microarray
wgs
updated 21 months ago by
Ram
43k • written 8.2 years ago by
DVA
▴ 630
13
votes
6
replies
4.4k
views
Why do people not call normal and tumor variant separately for somatic mutation identification?
snp
updated 8.2 years ago by
Chris Miller
22k • written 8.2 years ago by
DVA
▴ 630
0
votes
1
reply
2.1k
views
Read Orientations in IGV view of Bisulfite Sequencing
igv
bisulfite-sequencing
updated 19 months ago by
Ram
43k • written 8.6 years ago by
DVA
▴ 630
4
votes
8
replies
3.6k
views
Manually edit the flags in a sam file
sam
updated 19 months ago by
Ram
43k • written 8.6 years ago by
DVA
▴ 630
6
votes
12
replies
6.3k
views
Identify point mutations from each read in sam files
sam
mutations
updated 19 months ago by
Ram
43k • written 8.6 years ago by
DVA
▴ 630
4
votes
2
replies
4.0k
views
Question about Details in Picard MarkDuplicates
sequence
updated 16 months ago by
Ram
43k • written 8.8 years ago by
DVA
▴ 630
4
votes
2
replies
2.6k
views
Trouble obtaining chromosome number using standalone blastn
standalone-blast
blastn
alignment
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
DVA
▴ 630
49 results • Page
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