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3
votes
2
replies
1.7k
views
Tools to generate coverage plots for the sequenced virus reads
coverage SNP DNAseq Virus
updated 6.2 years ago by 20k • written 6.2 years ago by ▴ 370
0
votes
1
reply
1.8k
views
How to generate heatmap for differentially expressed genes based on the pathway?
RNA-SEQ heatmap differential expression
6.2 years ago by bioinforesearchquestions ▴ 370
0
votes
3
replies
1.5k
views
At which position, should I expect a peak for miRNA sequenced FASTQ reads?
miRNA RNA-seq smallRNA FASTQ
6.2 years ago by bioinforesearchquestions ▴ 370
2
votes
8
replies
2.5k
views
What is the acceptable percentage of reads with adapters sequenced in miRNA sequencing?
miRNA RNA-Seq smallRNA adapters Reads
6.2 years ago by bioinforesearchquestions ▴ 370
0
votes
0
replies
1.0k
views
Do I have to compared sequenced miRNA reads against bovine miRNA from miRBase mature.fa sequence or entire bovine genome?
miRNA small RNA RNA-seq
6.3 years ago by bioinforesearchquestions ▴ 370
6
votes
2
replies
2.9k
views
Which tool is recommended for detecting CNVs in whole exome sequencing?
CNVs WES whole exome sequencing
6.3 years ago by bioinforesearchquestions ▴ 370
3
votes
5
replies
2.4k
views
Is there any recommended steps/pipeline for identifying differential miRNA expression profile?
RNA-seq miRNA small RNA
6.3 years ago by bioinforesearchquestions ▴ 370
0
votes
1
reply
2.1k
views
How to filter out variants based on the population frequency
SNPs variants DNASeq Allele-frequency
updated 6.3 years ago by • 0 • written 7.3 years ago by ▴ 370
2
votes
2
replies
4.8k
views
Where to download fasta sequence of ribosomal RNAs for human build 37
sequencing alignment ribosomal rnas genome
6.3 years ago by bioinforesearchquestions ▴ 370
0
votes
0
replies
1.7k
views
How to compare genotype calls of the SNPS on chrom X for the GWAS samples between plink file vs Affymetrix genotype output file?
Affymetrix Plink PED Genotype GWAS
updated 6.4 years ago by 20 • written 6.4 years ago by ▴ 370
0
votes
0
replies
1.3k
views
Is there any tool to extract LD SNPs based on any other databases (except 1K database)?
snps LD 1000Genome mutations
6.5 years ago by bioinforesearchquestions ▴ 370
0
votes
1
reply
3.2k
views
Error while converting VCF output file from ERDS using convert2annovar.pl program
RNA-Seq sequencing next-gen SNP
updated 6.5 years ago by • 0 • written 7.1 years ago by ▴ 370
8
votes
9
replies
2.1k
views
When I am trying to copy 9GB BAM files to the hard disk, the copied BAM file has only 4GB.What could be the issue?
BAM Alignment DNASeq
6.6 years ago by bioinforesearchquestions ▴ 370
2
votes
8
replies
3.2k
views
How to cluster reads within the fastq file? Is their any tool?
alignment Assembly clustering fastq reads
updated 6.7 years ago by 35k • written 6.7 years ago by ▴ 370
0
votes
0
replies
1.5k
views
mirBase mature microRNA sequences have base U instead of base T. Should I change or not?
mirBase small RNA bowtie2 alignment
6.7 years ago by bioinforesearchquestions ▴ 370
5
votes
9
replies
13k
views
How to find On-Target and Off-Targer percentage of reads?
DNAseq Exome targeted sequencing bam
updated 6.7 years ago by ▴ 310 • written 6.7 years ago by ▴ 370
3
votes
5
replies
1.3k
views
Are there any tools which display SNPs inside each gene?
gene graphical DNAseq SNP
updated 6.9 years ago by ★ 3.6k • written 6.9 years ago by ▴ 370
5
votes
4
replies
5.0k
views
How to annotate CNV events with gene information?
SNP RNA DNA-seq CNV events annovar
updated 7.1 years ago by ★ 2.2k • written 7.1 years ago by ▴ 370
4
votes
8
replies
1.9k
views
Need suggestions on increasing the computational power for the bioinformatics analyses involving DNAseq, RNAseq, Chipseq pipeline
RNA-Seq SNP DNA-Seq next-gen
updated 7.1 years ago by ▴ 250 • written 7.1 years ago by ▴ 370
1
vote
6
replies
2.5k
views
Comparing splicing events and splicing junctions for cancer n normal samples from RNA-seq data
RNA-Seq rna-seq sequencing splicing
7.1 years ago by bioinforesearchquestions ▴ 370
1
vote
2
replies
3.7k
views
How to download the low mappability regions from the UCSC browser
DNA-seq RNA-seq CNV SNP
7.1 years ago by bioinforesearchquestions ▴ 370
2
votes
4
replies
1.3k
views
For RNAseq, is it mandatory to have approximately the same number of reads between the normal and cancer samples?
RNA-Seq
updated 7.2 years ago by ▴ 750 • written 7.2 years ago by ▴ 370
3
votes
2
replies
3.5k
views
Comparing the output from DESeq and DESeq2
RNA-Seq
updated 7.2 years ago by 13k • written 7.2 years ago by ▴ 370
3
votes
7
replies
2.7k
views
Differential gene expression based on read counts using DESeq package
RNA-Seq
updated 7.2 years ago by ★ 1.8k • written 7.2 years ago by ▴ 370
2
votes
3
replies
1.8k
views
Is my pair (1 cancer and 1 normal) considered as biological replicates?
RNA-Seq
updated 7.2 years ago by 13k • written 7.2 years ago by ▴ 370
1
vote
2
replies
2.1k
views
Queries regarding cuffdiff output especially gene_exp_diff (Tumor and Normal) no replicates
RNA-Seq rna-seq
7.2 years ago by bioinforesearchquestions ▴ 370
2
votes
5
replies
3.0k
views
What is the significance threshold for differential gene expression (10folds, 50folds, 100folds) between tumor and normal sample?
RNA-Seq
updated 7.2 years ago by 47k • written 7.2 years ago by ▴ 370
0
votes
0
replies
1.6k
views
What is the threshold vaue for mapping quality
snps indels DNASeq RNASeq
7.2 years ago by bioinforesearchquestions ▴ 370
2
votes
8
replies
4.9k
views
Genotype representation for male chromosome X and Y
snps dnaseq vcf genotype
7.3 years ago by bioinforesearchquestions ▴ 370
0
votes
3
replies
2.9k
views
Filtering multisample VCF based on genotype using SnpSift filter
VCF snpSift genotype DNASeq snps
updated 7.4 years ago by 41k • written 7.4 years ago by ▴ 370
1
vote
5
replies
4.7k
views
Is there a way to annotate existing VCF file with known disease-causing mutations?
VCF snps DNAseq
7.4 years ago by bioinforesearchquestions ▴ 370
0
votes
0
replies
2.7k
views
Comparing samtools,gatk and varscan against gold standard 1000G snps and need to decide the best method
snps vcfs DNAseq
updated 7.4 years ago by 20 • written 7.5 years ago by ▴ 370
0
votes
2
replies
2.3k
views
How do I change the settings in qualimap (bamqc) to consider only the exome length in every chromosome instead of entire chromosome length
sequencing bamqc bam coverage
7.4 years ago by bioinforesearchquestions ▴ 370
1
vote
2
replies
2.2k
views
For multisample VCF, should I filter the variants based on allele depth (AD) or Overall depth ?
VCFs SNPs Variants Depth DNASeq
updated 7.4 years ago by ▴ 180 • written 7.4 years ago by ▴ 370
2
votes
2
replies
4.2k
views
Need some clarifications in snpEFF annotation in extracting exonic variants
SNPs vcfs SNPEFF DNAseq
updated 7.5 years ago by ★ 1.3k • written 7.5 years ago by ▴ 370
8
votes
2
replies
15k
views
Where to find PCR duplicate reads in bam file?
bam dnaseq bwa bowtie2
updated 7.5 years ago by 158k • written 7.5 years ago by ▴ 370
0
votes
0
replies
2.6k
views
Trying to filter vcf file using SNPSIFT tool. It throws an error message
SNP VCFs SNPSIFT
7.5 years ago by bioinforesearchquestions ▴ 370
1
vote
5
replies
3.7k
views
Want to trim off last 50 bases from 151 bases read using trimmomatic?
FASTQ trimmomatic DNASeq RNASEq
updated 7.5 years ago by 13k • written 7.5 years ago by ▴ 370
0
votes
4
replies
2.1k
views
Individual vcf for each sample and single vcf for all samples. Does the output contents differ?
VCF SNP variant calling DNASeq RNASeq
7.5 years ago by bioinforesearchquestions ▴ 370
1
vote
3
replies
3.3k
views
Read counts based on genes from samtools, feature count and htseq-count
DNAseq featurecount samtools htseqcount
updated 7.6 years ago by 104k • written 7.6 years ago by ▴ 370
7
votes
10
replies
4.3k
views
Do I need to use hg19 or hg38 reference for performing variant calling analysis and RNAseq analysis?
SNP DNASeq RNASEq reference
updated 7.7 years ago by ▴ 90 • written 7.7 years ago by ▴ 370
5
votes
17
replies
10k
views
How to extract fasta sequence of a gene from BAM files generated using Miseq sequencing
gene Assembly sequencing BAM alignment
updated 16 months ago by 41k • written 7.8 years ago by ▴ 370
1
vote
5
replies
6.0k
views
What is mutation calling in exome sequencing?
Exome Mutation-calling SNP-calling Variant-calling
updated 16 months ago by 41k • written 8.0 years ago by ▴ 370
6
votes
11
replies
3.4k
views
Is there any differences between tophat, cufflinks command with and without GTF file?
cufflinks tophat rna-seq RNA-Seq
updated 2.1 years ago by 41k • written 8.1 years ago by ▴ 370
0
votes
3
replies
2.1k
views
How to filter and annotate variants for influenza virus?
VCF GATK SNP
updated 15 months ago by 41k • written 8.1 years ago by ▴ 370
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