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0
votes
2
replies
447
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Slideseq cell coordinate unit
Slideseq
10 months ago by morovatunc ▴ 550
1
vote
2
replies
3.7k
views
Downloading CHIP-seq bed files for ENCODE Histone modification data
ENCODE ChIP-Seq Histone Modifers
updated 17 months ago by ▴ 130 • written 8.2 years ago by ▴ 550
1
vote
2
replies
1.6k
views
Transcription Factor Specific Mutation Signature Enrichment
mutation signature r
updated 3.9 years ago by • 0 • written 7.0 years ago by ▴ 550
9
votes
15
replies
6.7k
views
Finding Chip Seq Overlaps with Bed files
bedops ChIP-Seq bedmap bedtools
updated 20 months ago by 43k • written 8.4 years ago by ▴ 550
2
votes
0
replies
1.1k
views
Amplicon based sequencing Mutation Calling
mutation calling sequence sequencing
5.6 years ago by morovatunc ▴ 550
1
vote
7
replies
8.9k
views
HOMER find motifs from BED data
ChIP-Seq Homer
updated 20 months ago by 43k • written 8.3 years ago by ▴ 550
2
votes
5
replies
1.1k
views
Starrseq data how can I characterise reads that maps out of the targeted regions.
alignment sequencing mapping starrseq
6.0 years ago by morovatunc ▴ 550
9
votes
8
replies
2.6k
views
Simplest output format of blast contamination check
blast megablast
updated 6.2 years ago by 35k • written 6.2 years ago by ▴ 550
0
votes
0
replies
2.3k
views
Bedtools -shuffle uniformly distributed bed regions
bedtools
updated 6.2 years ago by 20 • written 7.9 years ago by ▴ 550
3
votes
4
replies
1.4k
views
Sub-typing patients by a single gene's expression in TCGA dataset.
RNA-Seq TCGA
updated 6.2 years ago by ★ 2.2k • written 6.2 years ago by ▴ 550
0
votes
1
reply
1.1k
views
Designed primers with 3 bp mutations (codons) how to validate/visualize them?
blast bwa primer
6.2 years ago by morovatunc ▴ 550
0
votes
0
replies
2.1k
views
BWA aligner parameter tweaking to show primer mapping
bwa primer-design
6.3 years ago by morovatunc ▴ 550
4
votes
5
replies
6.4k
views
Chip-Seq Peak height difference between BED and BW file formats.
ChIP-Seq
updated 3.0 years ago by 43k • written 8.3 years ago by ▴ 550
0
votes
0
replies
1.3k
views
How should I compare multiple TF methylation percentages?
methylation encode TF
6.9 years ago by morovatunc ▴ 550
2
votes
2
replies
2.2k
views
Regular Expression help for (bcf/vcf)tools filter manipulation
vcftools bcftools
updated 6.9 years ago by ★ 2.8k • written 6.9 years ago by ▴ 550
3
votes
6
replies
1.5k
views
Could you suggest me a proper feature selection method for mixed type variable data?
machine learning
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 550
3
votes
2
replies
1.3k
views
about Mapability and Blacklisted regions?
mapability ucsc
updated 7.1 years ago by 104k • written 7.1 years ago by ▴ 550
1
vote
0
replies
1.4k
views
Proving spesific TF binding locations have mutation enrichment than rest of the binding sites statistically
ChIP-Seq Stat
7.1 years ago by morovatunc ▴ 550
0
votes
0
replies
1.2k
views
Checking TF binding region proximity mutational signature
mutation signature statistics
updated 7.1 years ago by 20 • written 7.1 years ago by ▴ 550
0
votes
0
replies
1.5k
views
ENCODE DNAse 1 HyperSensitivity Data - Signal of unique reads vs Base Overlap Signal vs Raw Signal
ENCODE
7.1 years ago by morovatunc ▴ 550
1
vote
4
replies
2.1k
views
Repeatmasker Annotation Descriptions
repeatmasker UCSC
updated 7.3 years ago by 20 • written 7.3 years ago by ▴ 550
0
votes
7
replies
1.5k
views
How can I set a feature based on a single mutation in specific location?
VCFTOOLS
7.3 years ago by morovatunc ▴ 550
0
votes
1
reply
1.6k
views
How can I go over a bed region based on peak name in UCSC Genome Browser?
UCSC BED
7.4 years ago by morovatunc ▴ 550
3
votes
5
replies
2.2k
views
How analyse chip-exo paired read data and get BigWig or Peaks called?
bedtools bed
updated 7.4 years ago by ▴ 580 • written 7.4 years ago by ▴ 550
0
votes
0
replies
1.5k
views
Visualisation of Multiple Alignment Files (MAFs) with IGV
IGV UCSC
7.4 years ago by morovatunc ▴ 550
0
votes
0
replies
2.0k
views
Visualisation of Binding Motifs on IGV (or any browser)
TF binding motif IGV
7.4 years ago by morovatunc ▴ 550
4
votes
4
replies
3.1k
views
Is okay to apply ANOVA to Log2 transformed data ?
ANOVA Statistics
updated 7.5 years ago by ▴ 940 • written 7.5 years ago by ▴ 550
0
votes
0
replies
1.6k
views
Calculating mutation significance of each location in a BED file.
VCF
7.6 years ago by morovatunc ▴ 550
1
vote
1
reply
3.8k
views
CRISPR screen Trimming with mageck low mappability
crispr screen trimming mapping
updated 7.6 years ago by 20 • written 7.8 years ago by ▴ 550
0
votes
1
reply
2.3k
views
Structural Variant Visualisation from VCF source.
RNA-Seq Circos VCF
7.6 years ago by morovatunc ▴ 550
9
votes
5
replies
2.8k
views
Any idea about validating bedtools shuffle did what I desired?
bedtools chip-seq
updated 7.6 years ago by 5.0k • written 7.6 years ago by ▴ 550
1
vote
4
replies
2.9k
views
IGV Visualisation Problem
IGV VCF snpsift vcftools
7.7 years ago by morovatunc ▴ 550
0
votes
6
replies
4.6k
views
Finding Overlapping Regions of Chip-Seq peaks, then visualising it.
ChIP-Seq Venn
updated 20 months ago by 43k • written 8.5 years ago by ▴ 550
0
votes
0
replies
1.3k
views
How to favor consistently occurring rare event in CRISPR screen analysis
CRISPR
7.7 years ago by morovatunc ▴ 550
0
votes
2
replies
2.3k
views
How to obtain peak height values from a bed file?
bedtools chip-seq
7.7 years ago by morovatunc ▴ 550
0
votes
0
replies
1.2k
views
Unlocalized contig visualisation and filtration for bed files.
bedtools Bed
7.8 years ago by morovatunc ▴ 550
1
vote
5
replies
1.5k
views
SnpSift match overlapping mutations with a given bed file
snpsift vcftools
7.8 years ago by morovatunc ▴ 550
4
votes
6
replies
4.2k
views
IGV peak Visualation Problem
ChIP-Seq IGv
updated 19 months ago by 43k • written 8.5 years ago by ▴ 550
0
votes
0
replies
1.5k
views
Vcftools where is my log file output ?
vcftools
7.8 years ago by morovatunc ▴ 550
1
vote
2
replies
1.9k
views
removing dbsnp for indel vcf
vcf
7.8 years ago by morovatunc ▴ 550
0
votes
0
replies
2.0k
views
VCF quaility score/filter assessment for ICGC vcf (by sanger pipeline)
vcf
7.8 years ago by morovatunc ▴ 550
1
vote
1
reply
1.5k
views
Coming with a result with many VCF files?
VCF variant-calling mutation-calling
updated 7.9 years ago by ★ 5.2k • written 8.0 years ago by ▴ 550
0
votes
5
replies
2.6k
views
VCF filtration problem No genotype information
Vcftools snpEff
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 550
4
votes
9
replies
1.6k
views
Increasing widths of the peaks in a bed file from ChIP-seq
ChIP-Seq vcftools mutation calling
updated 7.9 years ago by 104k • written 7.9 years ago by ▴ 550
0
votes
0
replies
1.5k
views
TCGA RNAseq Clustering validation
RNA-Seq
8.0 years ago by morovatunc ▴ 550
11
votes
4
replies
7.8k
views
Visualization of Homer mergePeaks output Venn?
overlap Venn euler HOMER ChIP-Seq
updated 20 months ago by 43k • written 8.5 years ago by ▴ 550
9
votes
4
replies
4.4k
views
GL000201,GL000202... etc What are these?
WGS ICGC BAM
updated 8.0 years ago by 13k • written 8.0 years ago by ▴ 550
1
vote
1
reply
1.8k
views
Mutational Calling with SomaticSeq
NGS somatic-mutations
updated 21 months ago by 43k • written 8.2 years ago by ▴ 550
2
votes
8
replies
2.1k
views
HOMER mergepeaks matrix interpreatation
ChIP-Seq
updated 8.0 years ago by 11k • written 8.0 years ago by ▴ 550
0
votes
2
replies
2.3k
views
Variant Calling output problem GL000 contigs
mutect vardict varscan freebayes
8.0 years ago by morovatunc ▴ 550
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