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78 results • Page
2 of 2
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votes
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131
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
2 days ago by
simplitia
▴ 130
0
votes
11
replies
509
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
2 days ago by
atowns21
• 0
0
votes
0
replies
106
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
2 days ago by
turcoa1
• 0
0
votes
0
replies
145
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
1 day ago by
HarperReed
• 0
0
votes
7
replies
324
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
GenoMax
141k • written 5 days ago by
Patadu94
• 0
0
votes
0
replies
100
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 1 day ago by
Ram
43k • written 1 day ago by
vanbelj
▴ 40
0
votes
0
replies
112
views
RNA-seq: full length gene
RNA-seq
updated 1 day ago by
Ram
43k • written 2 days ago by
Nargis
• 0
0
votes
3
replies
267
views
Highest variable features in single cell data
single-cell
updated 1 day ago by
bk11
★ 2.4k • written 2 days ago by
Kazo
• 0
0
votes
0
replies
116
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 1 day ago by
Ram
43k • written 1 day ago by
SineWave
• 0
0
votes
0
replies
298
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
1 day ago by
biocellbio
• 0
0
votes
5
replies
312
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 15 hours ago by
Istvan Albert
100k • written 3 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
57
views
Filter low express genes in microarray data
microarray
10 hours ago by
Chris
▴ 260
0
votes
0
replies
58
views
Extract protein sequence
fasta
alighment
blast
10 hours ago by
anna
▴ 20
0
votes
0
replies
55
views
How to assign cell types after integration in scRNA
integration
conditions
ScRNA
seq
9 hours ago by
Francesco
▴ 10
0
votes
0
replies
140
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 6 days ago by
Ram
43k • written 7 days ago by
sainavyav22
• 0
0
votes
0
replies
57
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
9 hours ago by
tnminh89
▴ 10
0
votes
2
replies
268
views
bam merging for archaic samples
samtools
bam
updated 6 days ago by
Ram
43k • written 7 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
132
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 5 days ago by
Carlo Yague
8.7k • written 6 days ago by
Atul K.
• 0
0
votes
0
replies
81
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
5 days ago by
Biostars2200
• 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
5 days ago by
sativus
▴ 20
0
votes
0
replies
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
5 days ago by
Enrique
• 0
0
votes
0
replies
74
views
Imputation advice
imputation
5 days ago by
kl
▴ 10
0
votes
0
replies
85
views
Annotating single cell data automatically
cell
annotation
single
5 days ago by
Gerard
• 0
0
votes
0
replies
85
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
5 days ago by
feather-W
• 0
0
votes
1
reply
155
views
RNA-seq bacteria contamination
RNA-seq
updated 5 days ago by
GenoMax
141k • written 5 days ago by
sh
• 0
0
votes
0
replies
88
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
5 days ago by
manaswwm
▴ 510
0
votes
1
reply
128
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 5 days ago by
ATpoint
82k • written 5 days ago by
enanoide
• 0
0
votes
0
replies
205
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
5 days ago by
Javier
• 0
78 results • Page
2 of 2
Recent Votes
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
correcting for a batch in DESeq2
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Recent Replies
Answer: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing?
by
GenoMax
141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
zihanss
• 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
by
Francesco
▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
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