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1
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0
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Discrepancy with MACS2.0 and MACS2.1 broad peaks
ChIP-Seq MACS2.1 MACS2
updated 2.7 years ago by 45k • written 9.4 years ago by ★ 5.2k
5
votes
12
replies
35k
views
How To Remove Rows In A Matrix Having 0 As Value In Columns In Both Conditions
r
updated 5.9 years ago by ▴ 30 • written 11.3 years ago by ★ 5.2k
13
votes
10
replies
2.7k
views
Is there a HGNC symbol or any ENSEMBLE/RefSeq ID for this UniProt : Rheumatoid factor C6 light chain?
gene mapping HGNC UniProt Ensembl
updated 6.0 years ago by ★ 2.4k • written 6.0 years ago by ★ 5.2k
0
votes
5
replies
4.7k
views
RNA-Seq data for Ovarian Cancers for a pilot experiment from public database
tcga RNA-Seq
updated 2.8 years ago by 45k • written 10.4 years ago by ★ 5.2k
3
votes
5
replies
3.9k
views
Somatic variants in exome normal/tumor data mostly in non-exonic regions. Is this a likely scenario?
snp Mutect SNPs next-gen
updated 3.3 years ago by 45k • written 10.7 years ago by ★ 5.2k
2
votes
3
replies
2.2k
views
Any suggestions upon re-quantifying bam files downloaded from EBI-EGA archive with Salmon?
salmon RNA-Seq rna-seq samtools bedtools
7.6 years ago by ivivek_ngs ★ 5.2k
0
votes
0
replies
1.7k
views
Downloading controlled access data from ICGC for specific ID?
icgc RNA-Seq
7.7 years ago by ivivek_ngs ★ 5.2k
2
votes
3
replies
2.3k
views
Query regarding the EBI ftp archive for SRA study SRP047194/PRJNA261255
sra fastq RNA-Seq ebi
7.8 years ago by ivivek_ngs ★ 5.2k
2
votes
5
replies
8.1k
views
Have anybody converted exome bam files to .tdf files for visualization in IGV?
sequencing alignment next-gen SNP
updated 3.5 years ago by 45k • written 10.8 years ago by ★ 5.2k
1
vote
0
replies
2.1k
views
Is it necessary to scale CpG data while using partitioning method and hierarchical clustering as a surrogate for reducing differentially methylated …
cpg RNA-Seq methylation kmeans clustering
7.9 years ago by ivivek_ngs ★ 5.2k
0
votes
0
replies
4.8k
views
Calling germline variants from Tumor/Clone pairs to find the somatic mutations of only tumor and only clone from the normal pair
next-gen SNP varscan2
updated 3.3 years ago by 45k • written 10.7 years ago by ★ 5.2k
4
votes
5
replies
4.1k
views
Is there any other way to separate CNVs from SNVs and MNVs from vcf file of Ion Reporter other than vcftools?
vcf vcftools SNP SNV CNV
updated 8.8 years ago by ★ 5.3k • written 8.8 years ago by ★ 5.2k
12
votes
13
replies
17k
views
7 follow
Can Anyone Suggest Me A Script Based Pipeline For Exome Sequencing With Paired End Reads Generated By Illumina For Tumor Samples.
ngs exome-sequencing programming
updated 2.1 years ago by 45k • written 11.6 years ago by ★ 5.2k
2
votes
0
replies
2.1k
views
Is it advisable to re-sequence ChIPSeq data having reads lower than 20 million for histone marks?
ChIP-Seq QC
9.0 years ago by ivivek_ngs ★ 5.2k
6
votes
4
replies
2.4k
views
Is there a database which gives meta-level information of mutation(both nuclueotide and AA change) for specific pathways?
exome-sequencing SNP pathway cancer
updated 2.8 years ago by 45k • written 9.2 years ago by ★ 5.2k
0
votes
1
reply
2.9k
views
Descrepancy with MACS model parameter for ChIP-Seq in tumor samples for Histone modifications
ChIP-Seq macs2 macs1.4 tumor
updated 2.6 years ago by 45k • written 9.6 years ago by ★ 5.2k
0
votes
0
replies
1.3k
views
Does anyone have a a sorted list of genes that are usually involved in chemosresistance?
chemoresistance RNA-Seq
updated 2.3 years ago by 45k • written 9.9 years ago by ★ 5.2k
1
vote
0
replies
2.2k
views
is it possible to define a window size in ADTex CNV tool?
cnv exome-seq ADtex
updated 2.8 years ago by 45k • written 10.0 years ago by ★ 5.2k
1
vote
0
replies
2.4k
views
Is there any falsepositive filter script for INDELS like the fpfilter.pl?
SNP sequence INDELS varscan2
updated 2.9 years ago by 45k • written 10.1 years ago by ★ 5.2k
0
votes
4
replies
2.3k
views
Isn't it strange to have similar CNV regions from iPSCs derived from 2 different tumor grades?
exome-sequencing CNV Control-FREEC
updated 2.8 years ago by 45k • written 10.0 years ago by ★ 5.2k
1
vote
4
replies
2.7k
views
Any GEO profile having Stage IV epithelial ovarian cancer samples for microarray having both normal and tumor samples
microarray ovarian cancer
updated 4.1 years ago by 45k • written 10.0 years ago by ★ 5.2k
2
votes
5
replies
2.7k
views
Error with bam-window
bam-window bam exome CNV
updated 2.8 years ago by 45k • written 10.1 years ago by ★ 5.2k
3
votes
9
replies
7.3k
views
Skipping The Local Realignment Around The Indels And Rather Aligning The Mapped Reads On The Exonic Region.
exome-sequencing gatk
updated 10.1 years ago by 8.3k • written 11.4 years ago by ★ 5.2k
4
votes
2
replies
3.5k
views
Sorting the cbioportal web output of oncoprint based on frequency percentage
cbioportal SNP CNV
updated 10.1 years ago by ▴ 50 • written 10.1 years ago by ★ 5.2k
3
votes
3
replies
7.7k
views
How can I convert a tab delemeted file to vcf format using vcf-annotate tool?
vcf vcftools snp tcga
updated 3.0 years ago by 45k • written 10.4 years ago by ★ 5.2k
0
votes
0
replies
1.9k
views
Annotating genomic coordinates of CNV regions with Lynx
annotation next-gen CNV
updated 3.0 years ago by 45k • written 10.2 years ago by ★ 5.2k
11
votes
9
replies
6.3k
views
Does multiIntersectBed works with -u and -f parameter?
bed sequencing bedtools intersect
updated 2.1 years ago by 45k • written 10.2 years ago by ★ 5.2k
2
votes
6
replies
3.3k
views
suggestions with bedtools interpretation with CNV bed files
sequencing cnv exome bedtools
updated 3.0 years ago by 45k • written 10.2 years ago by ★ 5.2k
1
vote
0
replies
2.3k
views
Is it possible to asses the significance of CNVs in ADtex like that of Control-FREEC?
sequencing ADtex FREEC CNV
updated 3.0 years ago by 45k • written 10.2 years ago by ★ 5.2k
5
votes
4
replies
6.7k
views
Finding significant overlap of mutations in a specific cancer tumors and its reprogrammed clones across all somatic mutation data from TCGA across al…
sequencing SNP tcga maf
updated 3.2 years ago by 45k • written 10.4 years ago by ★ 5.2k
1
vote
5
replies
3.9k
views
Need some help regarding format compatible with VEP online tools
SNP next-gen-sequencing
updated 3.2 years ago by 45k • written 10.5 years ago by ★ 5.2k
15
votes
22
replies
11k
views
Annotating variants with Annovar, Oncotator and SnpEFF
sequencing SNP
updated 3.2 years ago by 45k • written 10.5 years ago by ★ 5.2k
6
votes
11
replies
12k
views
How to export normalized read count in RLE method from edgeR?
next-gen edgeR RNA-Seq
updated 3.3 years ago by 45k • written 10.6 years ago by ★ 5.2k
10
votes
6
replies
5.7k
views
To remove genotype "./." from vcf file with awk
vcftools snp vcf
updated 3.5 years ago by 45k • written 10.8 years ago by ★ 5.2k
1
vote
7
replies
5.1k
views
Can VarScan be called with the Target kit bed files to emit more high confidence and specific somatic variants?
gatk MuTect SNP VarScan
updated 3.3 years ago by 45k • written 10.6 years ago by ★ 5.2k
1
vote
8
replies
5.6k
views
Discrepancy with Mutect output version 1.1.4 using the --interval option for normal/tumor pair cancer samples
MuTect GATK SNP
updated 3.2 years ago by 45k • written 10.6 years ago by ★ 5.2k
0
votes
2
replies
6.1k
views
Converting VarScan output (.txt) format to .vcf for annotation
vcf varscan2 SNP
updated 3.3 years ago by 45k • written 10.7 years ago by ★ 5.2k
0
votes
9
replies
4.8k
views
Annotation using annovar
annovar SNP
updated 3.3 years ago by 45k • written 10.7 years ago by ★ 5.2k
9
votes
13
replies
14k
views
6 follow
Rna-Seq Data Normalization With Spike-In Using Deseq
differential-expression r
updated 3.2 years ago by 45k • written 11.7 years ago by ★ 5.2k
3
votes
5
replies
8.2k
views
CNV calling with Control-FREEC? Significant calls
FREEC CNV SNP NGS
updated 3.4 years ago by 45k • written 10.7 years ago by ★ 5.2k
5
votes
16
replies
6.6k
views
Identifying the tumor clones and subclones with VAF from VarScan2
exome sequencing SNP next-gen
updated 3.5 years ago by 45k • written 10.8 years ago by ★ 5.2k
1
vote
1
reply
2.8k
views
Can we do unsupervised clustering of Varscan output based on variant frequencies?
varscan2 next-gen exome-sequencing varscan
updated 3.6 years ago by 45k • written 11.0 years ago by ★ 5.2k
0
votes
4
replies
4.1k
views
Can anyone tell me the frequency percentage given by varscan2 is for individual or global?
SNP next-gen sequencing
updated 3.5 years ago by 45k • written 10.9 years ago by ★ 5.2k
1
vote
2
replies
3.9k
views
Error With Unifiedgenotyper With Option -Glm Both With Gatk During Variant Calling
gatk exome exome-sequencing
updated 10.9 years ago by 20 • written 11.5 years ago by ★ 5.2k
5
votes
5
replies
4.9k
views
Help With The Dnacopy Number Package In R
exome-sequencing
updated 11.1 years ago by 27k • written 11.1 years ago by ★ 5.2k
1
vote
0
replies
3.0k
views
Can We Call Variants Based On Alt Allele Frequncy?
gatk exome-sequencing annovar varscan
updated 11.1 years ago by 22k • written 11.1 years ago by ★ 5.2k
1
vote
9
replies
3.3k
views
Can We Compare The Total Reads Between Tumor And Its Wild Type Before Calling Variants To Check Globally Landscape Of Tumor/Wild Type/Ips?
exome-sequencing reads variant-calling
updated 11.2 years ago by 3.5k • written 11.2 years ago by ★ 5.2k
2
votes
4
replies
4.6k
views
Can We Call The Variants Using Haplotype Caller Or Unified Genotyper Without Dbsnp Vcf File?
exome-sequencing variant-calling gatk
updated 3.8 years ago by 45k • written 11.2 years ago by ★ 5.2k
1
vote
2
replies
4.5k
views
Which To Consider As Non-Sense Mutation From Annovar Output?
annovar exome-sequencing gatk
updated 11.2 years ago by 12k • written 11.2 years ago by ★ 5.2k
1
vote
4
replies
4.8k
views
To Understand The Output Of The Diagnosetarget And Depthofcoverage Walker In Gatk
exome-sequencing gatk qc
updated 11.3 years ago by ▴ 10 • written 11.4 years ago by ★ 5.2k
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