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4
votes
2
replies
312
views
How can I check if a variant affects a TFBS?
variant TFBS
3 months ago by Tania ▴ 180
2
votes
2
replies
4.2k
views
Insert size is so small, good or bad?
Insert-size RNA-Seq
updated 16 months ago by 44k • written 7.2 years ago by ▴ 180
0
votes
0
replies
352
views
Can we use logFC MLE for pathway analysis instead of logFC?
rnaseq dge
2.6 years ago by Tania ▴ 180
5
votes
6
replies
1.3k
views
Is 60,000 estimated cell per sample in sn/scRNASeq too high?
scsnRNASeq
2.6 years ago by Tania ▴ 180
3
votes
4
replies
920
views
Percentage of mitochondoria in single nuclei single cellRNASeq
cell mitochondoria nuclei single RNASeq
2.6 years ago by Tania ▴ 180
1
vote
2
replies
746
views
Weird over-represented sequence in sn/scRNASeq fastqc
single cell nuclei FASTQC RNASeq
2.6 years ago by Tania ▴ 180
3
votes
3
replies
1.6k
views
BBMap Clumpify error
mark duplicates
4.6 years ago by Tania ▴ 180
6
votes
21
replies
4.4k
views
6 follow
GT 2/3, or 3/3 or 2/2 in vcf
vcf
updated 4.7 years ago by ▴ 940 • written 4.7 years ago by ▴ 180
1
vote
2
replies
1.4k
views
Genotype dosage tools
vcf genotype dosage
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 180
1
vote
6
replies
1.5k
views
cufflinks transcripts to ensemble or NCBI transcript
rna-seq
updated 4.8 years ago by 20 • written 6.8 years ago by ▴ 180
0
votes
1
reply
2.2k
views
How can we find the list of genes involved in each pathway using Gage?
RNA-Seq Pathways Gage
updated 5.7 years ago by • 0 • written 7.0 years ago by ▴ 180
3
votes
2
replies
5.6k
views
BaseQRankSum and FS
VCF ARTIFACTS
updated 6.2 years ago by ▴ 390 • written 6.9 years ago by ▴ 180
3
votes
7
replies
6.8k
views
Salmon very low mapping
RNA-Seq Salmon
updated 6.3 years ago by 20 • written 7.2 years ago by ▴ 180
0
votes
0
replies
1.3k
views
Check CNV analysis from CNVnator
CNV exome whole genome
updated 6.3 years ago by 20 • written 6.4 years ago by ▴ 180
2
votes
7
replies
5.4k
views
How to remove duplicate SNPs from plink ped,vcf?
SNP plink
updated 6.6 years ago by 88k • written 6.6 years ago by ▴ 180
5
votes
8
replies
4.6k
views
Does high or low GC content affect base quality?
RNA-Seq
6.6 years ago by Tania ▴ 180
1
vote
6
replies
2.4k
views
Help understand RNAseq deconvolution results?
RNA-Seq
6.7 years ago by Tania ▴ 180
8
votes
9
replies
1.8k
views
Coverage in whole genome sequencing
WGS Coverage
updated 6.7 years ago by ▴ 610 • written 6.7 years ago by ▴ 180
0
votes
2
replies
1.2k
views
Mappability in duplicate gene?
exome sequencing variant calling
6.7 years ago by Tania ▴ 180
4
votes
5
replies
3.8k
views
add gene names in bed file
BED annotations
updated 6.7 years ago by 36k • written 6.7 years ago by ▴ 180
6
votes
11
replies
2.0k
views
How low is OK to accept variants in high/low GC content regions?
VCF Exome sequencing
updated 6.7 years ago by 88k • written 6.7 years ago by ▴ 180
3
votes
4
replies
4.1k
views
CosmicCodingMuts.vcf.gz for hg38?
RNA-Seq SomaticMutations
updated 6.8 years ago by 20 • written 6.9 years ago by ▴ 180
5
votes
3
replies
1.4k
views
Should we ignore variants in any duplicated gene, or only ignore variants in duplicated segments?
Variant calling
6.8 years ago by Tania ▴ 180
0
votes
4
replies
1.6k
views
Is there a full one link for exome raw fastq to vcf pipleine in gatk?
exome data variant calling
updated 6.9 years ago by 165k • written 6.9 years ago by ▴ 180
20
votes
26
replies
7.3k
views
9 follow
Is there a better tool for visualizing your variants after annotation than Excel?
annotations variants
updated 2.4 years ago by 165k • written 6.9 years ago by ▴ 180
5
votes
10
replies
3.0k
views
Can't find a pattern in heatmap, is it okay?
RNA-Seq heatmap
6.9 years ago by Tania ▴ 180
0
votes
0
replies
1.8k
views
Can we omit the normal input and compare tumor to pon only in MuTect2?
Tumor RNA-Seq mutect
6.9 years ago by Tania ▴ 180
1
vote
11
replies
2.3k
views
pvalues very low in Salmon and edgeR
RNA-Seq
updated 7.0 years ago by 20 • written 7.2 years ago by ▴ 180
1
vote
1
reply
1.0k
views
Low frequent variants in SINE regions?
Variants SINE-Region
updated 2.6 years ago by 44k • written 7.0 years ago by ▴ 180
1
vote
7
replies
2.4k
views
BBMap output meaning
bbmap rnaseq
updated 7.0 years ago by 20 • written 7.2 years ago by ▴ 180
5
votes
14
replies
2.0k
views
Interpretation for lowfrevariant
vcf
7.0 years ago by Tania ▴ 180
0
votes
3
replies
2.8k
views
NA in pathways gage values
Pathways
updated 12 months ago by • 0 • written 7.0 years ago by ▴ 180
9
votes
8
replies
2.5k
views
Up and down pathways are the same?
pathways gage
updated 7.0 years ago by 27k • written 7.0 years ago by ▴ 180
4
votes
9
replies
2.9k
views
Can't fetch pathways by entrez id?
Gage Pathways
7.1 years ago by Tania ▴ 180
4
votes
4
replies
1.6k
views
How to select tumor GO terms, if I did not find any in my biological process GO terms?
RNASeq GO
7.1 years ago by Tania ▴ 180
8
votes
12
replies
2.6k
views
Help fixing my DGE heatmap?
RNA-Seq Heatmap
updated 7.1 years ago by 88k • written 7.1 years ago by ▴ 180
1
vote
2
replies
1.5k
views
Explaining gene ontology results by gage ?
RNA-Seq Gene ontology
updated 7.1 years ago by ▴ 610 • written 7.1 years ago by ▴ 180
3
votes
4
replies
6.0k
views
What is my RGID, RGLB and RGPU in this read, please?
RNA-Seq
updated 7.1 years ago by ▴ 610 • written 7.1 years ago by ▴ 180
0
votes
0
replies
1.3k
views
What is the difference between paired and unpaired and same.dir is true or false in Gage?
RNA-Seq Gage Pathway analysis
7.1 years ago by Tania ▴ 180
2
votes
4
replies
2.0k
views
should we ignore interesting variants with no MAF in gnomAD or ExAC by annovar?
variants annovar
updated 7.1 years ago by 47k • written 7.1 years ago by ▴ 180
4
votes
9
replies
4.7k
views
Tximport mixing annotations
RNA-Seq tximport txdb
7.2 years ago by Tania ▴ 180
2
votes
7
replies
2.5k
views
edgeR steps for gene expressions
RNA-Seq
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by ▴ 180
1
vote
2
replies
3.4k
views
Help in tximport
RNAseq tximport
updated 7.2 years ago by 47k • written 7.2 years ago by ▴ 180
3
votes
10
replies
2.3k
views
How low is too low mapping to proceed with differential expression analysis?
RNA-Seq salmon mapping
updated 7.2 years ago by 105k • written 7.2 years ago by ▴ 180
3
votes
10
replies
4.7k
views
Adapter percentages in the reads
RNA-Seq Trimgalore cutadapt
updated 7.2 years ago by 148k • written 7.2 years ago by ▴ 180
3
votes
3
replies
2.5k
views
Does insert size short length affect mapping rate?
RNA-Seq low mapping rate small insert size
7.2 years ago by Tania ▴ 180
1
vote
4
replies
1.9k
views
Conservation of amino acid
AMINO ACID CONSERVATION
7.2 years ago by Tania ▴ 180
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