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Showing :
questions
0
votes
4
replies
356
views
bcftools select sites with multiple combinations of FILTER column
bcftools
6 days ago by
User000
▴ 690
0
votes
0
replies
400
views
Analyse UMI using picard's ExtractIlluminaBarcodes & IlluminaBasecallsToSam with 2 or 4 lanes
picard
umi
10 months ago by
User000
▴ 690
0
votes
1
reply
678
views
How to remove from BAM file header all chromosomes, except chrM
samtools
updated 9 months ago by
Ram
43k • written 14 months ago by
User000
▴ 690
1
vote
1
reply
492
views
DepthOfCoverage badly formed genome location error
coverage
updated 12 months ago by
Fabio Marroni
★ 3.0k • written 14 months ago by
User000
▴ 690
1
vote
6
replies
2.6k
views
Bedtools coverage histogram
bedtools
updated 16 months ago by
ED
• 0 • written 2.8 years ago by
User000
▴ 690
0
votes
0
replies
594
views
Getting the mean normalized expression values of mutants and controls in DESeq2 prior calculation of Log2FC
DESeq2
RNAseq
Log2FC
18 months ago by
User000
▴ 690
0
votes
2
replies
1.0k
views
g.vcf file with different FORMAT (GT:AD:DP:GQ:PL:SB vs GT:DP:GQ:MIN_DP:PL)
vcf
23 months ago by
User000
▴ 690
1
vote
0
replies
485
views
How to get sample names and genotype for SNP in multi-sample VCF file with special occurence
vcf
24 months ago by
User000
▴ 690
7
votes
8
replies
3.0k
views
bcftools query add header
bcftools
updated 14 months ago by
jon.klonowski
▴ 150 • written 24 months ago by
User000
▴ 690
3
votes
8
replies
948
views
Merge two files with multiple columns by 4 common columns
vcf
updated 2.0 years ago by
cpad0112
21k • written 2.0 years ago by
User000
▴ 690
5
votes
9
replies
1.6k
views
Extract only first individual from vcf files
vcf
updated 2.1 years ago by
cpad0112
21k • written 2.1 years ago by
User000
▴ 690
5
votes
5
replies
1.3k
views
Enrichment plot in R with custom pathways
RNAseq
DESeq2
enrichplot
R
updated 2.2 years ago by
Jean-Karim Heriche
27k • written 2.2 years ago by
User000
▴ 690
8
votes
7
replies
6.2k
views
Split multiallelic SNPs to biallelic from vcf
python
R
bash
vcf
updated 2.2 years ago by
DareDevil
★ 4.3k • written 3.1 years ago by
User000
▴ 690
2
votes
4
replies
1.5k
views
DESeq2 contrast multiple treated conditions versus multiple control conditions
RNAseq
DESeq2
2.2 years ago by
User000
▴ 690
1
vote
0
replies
739
views
Enrichplot heatplot label_format does not work
enrichplot
DESeq2
heatplot
RNAseq
2.5 years ago by
User000
▴ 690
7
votes
7
replies
3.1k
views
DESeq2 log2FC and p-value filtering
DESeq2
RNAseq
updated 2.5 years ago by
i.sudbery
18k • written 2.5 years ago by
User000
▴ 690
0
votes
0
replies
663
views
DESeq2 treated vs untreated and contrast vs no contrast
DESeq2
RNAseq
2.5 years ago by
User000
▴ 690
16
votes
15
replies
11k
views
8 follow
BAM files compression
bam
updated 2.7 years ago by
Divon
▴ 230 • written 4.1 years ago by
User000
▴ 690
2
votes
2
replies
1.2k
views
DESeq2 results difference using contrast and single conditions
DESeq2
RNAseq
2.7 years ago by
User000
▴ 690
5
votes
4
replies
1.1k
views
Convert missing genotype ./. to homozygous 0/0 in vcf
vcf
updated 2.7 years ago by
sbstevenlee
▴ 480 • written 2.7 years ago by
User000
▴ 690
4
votes
7
replies
1.6k
views
Should we keep only the uniquely mapped reads for gene expression
RNA-seq
updated 2.8 years ago by
jared.andrews07
★ 16k • written 2.8 years ago by
User000
▴ 690
2
votes
7
replies
1.0k
views
Count the numfer of reads supporting a pattern from a BAM file
samtools
updated 2.8 years ago by
jkbonfield
★ 1.2k • written 2.8 years ago by
User000
▴ 690
8
votes
9
replies
2.6k
views
Extract reads overlapping a specific region in bam file
awk
samtools
updated 23 months ago by
hopf
▴ 10 • written 2.9 years ago by
User000
▴ 690
0
votes
0
replies
512
views
Correlation test based on position sliding window for multiple variables
statistics
R
corr.test
3.0 years ago by
User000
▴ 690
7
votes
19
replies
3.2k
views
DNA sequence complexity with a sliding window
R
python
dna
updated 3.0 years ago by
GenoMax
140k • written 3.0 years ago by
User000
▴ 690
1
vote
5
replies
941
views
BCFTools query regex or boolean expression
bcftools
3.1 years ago by
User000
▴ 690
5
votes
5
replies
3.8k
views
Running BLAST on huge files
alignment
blast
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
User000
▴ 690
2
votes
6
replies
1.5k
views
Platypus variant caller error
SNP
variant calling
3.3 years ago by
User000
▴ 690
1
vote
6
replies
2.7k
views
VCF parse error: Could not add dummy header for contig
vcf
freebayes
3.3 years ago by
User000
▴ 690
0
votes
0
replies
608
views
Platypus variant calling outputs VCFv4.0 with no contig ID
vcf
3.3 years ago by
User000
▴ 690
2
votes
7
replies
1.8k
views
Interval list as a wildcard in snakemake
snakemake
wildcards
3.4 years ago by
User000
▴ 690
4
votes
4
replies
2.1k
views
Variant calling from FASTA file
bwa
bowtie
fasta
vcf
3.4 years ago by
User000
▴ 690
5
votes
7
replies
2.5k
views
GATK variant calling on multiple bam files
gatk
bam
3.4 years ago by
User000
▴ 690
2
votes
7
replies
2.1k
views
Freebayes variant calling understanding
freebayes
SNP
updated 3.4 years ago by
Biostar
20 • written 4.1 years ago by
User000
▴ 690
0
votes
0
replies
652
views
Merging the libraries
BAM
merge
readgroupname
3.5 years ago by
User000
▴ 690
5
votes
14
replies
2.4k
views
Samtools merge BAM files using snakemake
samtools
snakemake
bam
updated 3.6 years ago by
Devon Ryan
104k • written 3.6 years ago by
User000
▴ 690
1
vote
6
replies
2.8k
views
Replace heterozygous GT to missing in vcf file using bcftools
bcftools
vcf
3.7 years ago by
User000
▴ 690
4
votes
8
replies
1.4k
views
It is possible to get gzipped fastq.gz files as output in SABRE?
sabre
demultiplex
updated 3.8 years ago by
Pierre Lindenbaum
160k • written 3.8 years ago by
User000
▴ 690
0
votes
0
replies
732
views
Freebayes adjusting parameters to "force" homozygous call
freebayes
variant calling
updated 3.9 years ago by
Biostar
20 • written 4.1 years ago by
User000
▴ 690
9
votes
16
replies
4.7k
views
Imputation with BEAGLE 5.1 giving an inconsistent number of alleles error
freebayes
beagle
updated 14 months ago by
yzliu01
▴ 10 • written 3.9 years ago by
User000
▴ 690
1
vote
11
replies
1.2k
views
Extract several columns from a VCF file
vcf
updated 4.1 years ago by
tacrolimus
▴ 140 • written 4.1 years ago by
User000
▴ 690
3
votes
8
replies
1.7k
views
Bedtools intersect/bcftools annotate dublicate the SNPs
bcftools
bedtools
SNP
4.1 years ago by
User000
▴ 690
4
votes
1
reply
2.5k
views
Bcftools filtering only 10% missing and heterozygous calls
bcftools
4.1 years ago by
User000
▴ 690
0
votes
0
replies
1.3k
views
Picard AddOrReplaceReadGroups for multiple BAM files
picard
SNP
4.1 years ago by
User000
▴ 690
0
votes
6
replies
2.9k
views
Bedtools intersect vcf and bed files
bedtools
bcftools
SAM
4.1 years ago by
User000
▴ 690
0
votes
0
replies
1.8k
views
Path to bam files in --bam_list bcftools mpileup
bcftools
bam
4.1 years ago by
User000
▴ 690
3
votes
4
replies
1.1k
views
Extract SNPs from VCF file located in genes or flanking +/- 5Kbp on GFF file
vcf
gff
bedtools
updated 4.1 years ago by
jared.andrews07
★ 16k • written 4.1 years ago by
User000
▴ 690
5
votes
8
replies
5.2k
views
BWA mem bam output name sorted
bam
bwa
samtools
updated 4.1 years ago by
ATpoint
81k • written 4.1 years ago by
User000
▴ 690
7
votes
21
replies
5.7k
views
bwa mem memory allocation, threads and nodes
bwa
updated 4.1 years ago by
d-cameron
★ 2.9k • written 4.1 years ago by
User000
▴ 690
5
votes
12
replies
3.0k
views
BWA MEM using snakemake
snakemake
bwa
4.2 years ago by
User000
▴ 690
94 results • Page
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