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How to create GTF file for virus and build database for influenza virus using annovar for annotating virus variants?
variants annovar SNP
updated 15 months ago by 41k • written 8.1 years ago by ▴ 370
0
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2
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8.9k
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Applying hard filters for variants
variants variant-calling GATK snps
updated 15 months ago by 41k • written 8.1 years ago by ▴ 370
3
votes
3
replies
2.9k
views
Do I need to download any specific adapters for Illumina small RNA sequencing kit?
Adapter trimming small RNA trimmomatic cutadapt
updated 2.6 years ago by 136k • written 6.7 years ago by ▴ 370
1
vote
6
replies
812
views
Can we use CRAM files for Telomerecat?
whole genome sequence
3.0 years ago by bioinforesearchquestions ▴ 370
2
votes
6
replies
3.1k
views
How to create bigwig using mm10.fasta and mm10.fasta bowtie index files
bigwig wig mouse HMMcopy
updated 3.1 years ago by • 0 • written 5.8 years ago by ▴ 370
14
votes
11
replies
9.8k
views
How many PCs should be considered for downstream analyses?
scRNAseq PCA UMAP Clustering RNAseq
updated 3.2 years ago by ▴ 170 • written 3.8 years ago by ▴ 370
3
votes
13
replies
1.3k
views
How to Normalize the effect between group in bulk RNAseq?
RNA-Seq Normalize Drug treatment
3.6 years ago by bioinforesearchquestions ▴ 370
3
votes
2
replies
4.4k
views
Tutorials: Trajectory analysis using Velocity
singlecell 10X velocity trajectory
3.6 years ago by bioinforesearchquestions ▴ 370
10
votes
7
replies
2.5k
views
Help required for Bacterial RNAseq data
RNAseq gene expression
updated 3.7 years ago by ▴ 10 • written 6.2 years ago by ▴ 370
8
votes
5
replies
5.7k
views
Downsampling one of the sample on the UMAP clustering to match the number of cells of the other group
scRNAseq UMAP downsampling RNAseq
updated 3.8 years ago by ★ 16k • written 3.8 years ago by ▴ 370
0
votes
0
replies
887
views
How to find percentage of a gene (eg.Ppbp) for condition A and condition B from 10X Single Cell RNAseq?
single cell RNAseq 10X cellranger
updated 3.9 years ago by 20 • written 4.0 years ago by ▴ 370
4
votes
4
replies
13k
views
Heatmap with custom gene labels annotated on the rows
RNAseq heatmap differential gene expression Bulk
4.3 years ago by bioinforesearchquestions ▴ 370
4
votes
18
replies
2.3k
views
Comparing the WG sequenced isolate against the other same genus isolates on the public database
alignment WGS SNPs BLAST bacteria
updated 4.3 years ago by ▴ 50 • written 4.3 years ago by ▴ 370
3
votes
5
replies
5.3k
views
How to customize the MA Plot (DESeq2) with some gene to be labelled
RNAseq MA plot RNA-Seq
updated 4.3 years ago by 41k • written 4.3 years ago by ▴ 370
1
vote
2
replies
891
views
What will be the impact of strandedness on differentially expressed genes?
RNAseq stranded expression DE
updated 4.3 years ago by 35k • written 4.3 years ago by ▴ 370
10
votes
7
replies
5.3k
views
Could not find rRNA genes (28S, 18S, 5.8S and 5S) in human_genes.gtf file?
gene GTF rRNA RNA-seq
updated 15 months ago by 41k • written 8.1 years ago by ▴ 370
0
votes
5
replies
1.5k
views
Error in cummeRbund R library package (Error: Columns index not found)
RNAseq cummeRbund cuffdiff
updated 4.5 years ago by ▴ 60 • written 5.2 years ago by ▴ 370
3
votes
9
replies
6.3k
views
Should I consider contigs.fa or scaffolds.fa from SPAdes output for downstream analyses?
Assembly SPAdes contigs QUAST
updated 4.5 years ago by 35k • written 4.5 years ago by ▴ 370
5
votes
7
replies
2.2k
views
Kmer selection for bacterial WGS denovo assembly using SPAdes or SOAP-denovo
Assembly SPAdes Soap-denovo WGS bacterial
updated 4.5 years ago by 35k • written 4.5 years ago by ▴ 370
2
votes
1
reply
1.1k
views
Identify AMR genes from WGS bacterial sequence
WGS bacteria AMR genome assembly
updated 4.5 years ago by ▴ 310 • written 4.5 years ago by ▴ 370
8
votes
8
replies
1.6k
views
How to find pathogenicity of a single missense variant ?
SNP sift polyphen2
updated 4.6 years ago by 86k • written 4.6 years ago by ▴ 370
0
votes
0
replies
866
views
Is there any other options to fetch the rs-ids for the markers for the Illumina custom array?
SNP illumina iScan rsids dbsnp
4.6 years ago by bioinforesearchquestions ▴ 370
1
vote
2
replies
3.8k
views
What does yield refer to in demultiplexing statistics
NGS fastq RNA-seq
updated 15 months ago by 41k • written 8.1 years ago by ▴ 370
3
votes
8
replies
1.2k
views
Selecting methods for performing pairwise RNAseq analysis without replicates
rna-seq DESeq2 DESeq Hisat2 tissues
updated 4.8 years ago by 18k • written 4.8 years ago by ▴ 370
0
votes
2
replies
992
views
Identifying consensus sequence between multiple Arabidopsis genome sequences
Alignment Consensus SNPs Variations Plant
5.0 years ago by bioinforesearchquestions ▴ 370
10
votes
8
replies
2.4k
views
Pathway analysis and Gene enrichment Analysis Queries
RNAseq Pathway analysis Enrichment score GSEA
updated 5.0 years ago by ▴ 120 • written 5.0 years ago by ▴ 370
3
votes
4
replies
9.3k
views
How to download VCF of 1000 genome project with population frequencies?
SNPs 1000Genome VCF rsids
updated 5.1 years ago by 16k • written 5.1 years ago by ▴ 370
2
votes
2
replies
2.1k
views
I have some queries on coverage
coverage RNASeq DNAseq SNP
updated 5.2 years ago by 41k • written 7.8 years ago by ▴ 370
5
votes
1
reply
2.5k
views
Which one do I need to consider single-read or multi-read mappability bigwig file for creating mouse mappability file?
Mappability mouse mm10 mm9 HMMcopy
updated 5.3 years ago by ▴ 220 • written 5.8 years ago by ▴ 370
1
vote
1
reply
1.0k
views
how to evaluate coverage at a regions of interest and generate specificity, sensitivity and PPV for that region?
SNP DNAseq specificity sensitivity PPV
updated 5.3 years ago by 20 • written 5.4 years ago by ▴ 370
7
votes
7
replies
5.1k
views
What is the appropriate assembler for PacBio long reads
Assembly alignment
updated 5.3 years ago by ▴ 370 • written 5.3 years ago by ▴ 370
1
vote
2
replies
2.0k
views
Are there any tools for comparing structural variants between different callers?
Structural variants SV
5.4 years ago by bioinforesearchquestions ▴ 370
5
votes
2
replies
1.2k
views
How to align the sanger sequenced fragments against human reference gene?
DNAseq sanger align alignment
updated 5.5 years ago by 47k • written 5.5 years ago by ▴ 370
0
votes
2
replies
1.5k
views
While generating the % of mapped reads to all miRNAs, do I need to consider unique or multi-match reads?
miRNA mirdeep2 RNAseq
5.6 years ago by bioinforesearchquestions ▴ 370
0
votes
2
replies
1.7k
views
Need help in selecting the correct output file from miRDeep2?
miRNA miRDeep2 miRBase RNA-Seq
5.6 years ago by bioinforesearchquestions ▴ 370
1
vote
1
reply
2.2k
views
how to annotate (rRNA, tRNA, Mt_rRNA, Mt_tRNA, etc) sequenced small RNA reads
rna-seq small RNA annotation
5.6 years ago by bioinforesearchquestions ▴ 370
0
votes
2
replies
1.8k
views
What are the methods to downsample the Depth of coverage (ex: 50X -> 25X)?
BAM downsample depth wig
5.6 years ago by bioinforesearchquestions ▴ 370
5
votes
5
replies
5.4k
views
How to visualize large VCF files
VCF variant calling SNPS SNP variant
updated 5.7 years ago by 20 • written 7.5 years ago by ▴ 370
1
vote
3
replies
1.4k
views
Need tools recommendation for plant RNAseq data
RNA-Seq plants Assembly variant calling
updated 5.8 years ago by ▴ 150 • written 5.8 years ago by ▴ 370
2
votes
1
reply
985
views
Is it possible to check whether a sample is progeny of the other two samples from exome sequenced data?
SNP exome NGS DNA-SEQ
updated 5.8 years ago by ▴ 600 • written 5.8 years ago by ▴ 370
10
votes
14
replies
4.0k
views
6 follow
How to validate the SNP calling pipeline?
DNASeq variant calling SNP
updated 5.8 years ago by 86k • written 5.8 years ago by ▴ 370
1
vote
13
replies
2.5k
views
How to generate FASTA sequence of genes and phylogenetic analysis from NGS sequenced reads?
DNAseq FASTA Phylogenetic analysis NGS
updated 5.8 years ago by 20 • written 5.9 years ago by ▴ 370
2
votes
5
replies
3.7k
views
Do I need to provide the Illumina's target region bed file for qualimap?
dnaseq coverage depth exome sequencing WES
updated 5.9 years ago by ★ 1.3k • written 6.1 years ago by ▴ 370
2
votes
1
reply
3.3k
views
Which read counts file from miRDeep2 should be considered for differential expression analysis?
miRNA miRDeep2 miRBase RNA-Seq
updated 5.9 years ago by 35k • written 6.1 years ago by ▴ 370
4
votes
7
replies
1.9k
views
What kind of filtering can be applied to reduce my exonic variants?
Exomeseq SNP DNAseq Trio Variants
updated 6.0 years ago by 20 • written 6.7 years ago by ▴ 370
0
votes
0
replies
1.6k
views
Looking for WIG base coverage file for hg19 to call CNVs in Exome data using EXCAVATOR
CNV Exome EXCAVATOR WIG hg19
6.1 years ago by bioinforesearchquestions ▴ 370
1
vote
2
replies
1.9k
views
Can I merge the exome interval lists from two different kits for identifying CNVs using XHMM?
CNVs BED Exome XHMM Intervals
updated 6.1 years ago by 26k • written 6.1 years ago by ▴ 370
8
votes
6
replies
2.9k
views
How come the QC-passed reads from samtools flagstat is different from FASTQ (R1+R2) read count?
samtools sam bam alignment
updated 6.1 years ago by 5.8k • written 6.1 years ago by ▴ 370
6
votes
13
replies
2.6k
views
What is the difference between log2(Mutant/Wildtype) or log2(Wildtype/Mutant) from cuffdiff output?
RNA-SEQ heatmap cuffdiff
updated 6.2 years ago by ★ 2.2k • written 6.2 years ago by ▴ 370
10
votes
9
replies
6.1k
views
How to cluster the upregulated and downregulated genes in heatmap?
RNA-SEQ heatmap
updated 6.2 years ago by 86k • written 6.2 years ago by ▴ 370
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