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84 results • Page
2 of 2
Sort: Votes
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Votes
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0
votes
11
replies
524
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How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
3 days ago by
atowns21
• 0
0
votes
0
replies
141
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
3 days ago by
turcoa1
• 0
0
votes
0
replies
178
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
2 days ago by
HarperReed
• 0
0
votes
7
replies
333
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
GenoMax
141k • written 6 days ago by
Patadu94
• 0
0
votes
0
replies
147
views
RNA-seq: full length gene
RNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
Nargis
• 0
0
votes
3
replies
277
views
Highest variable features in single cell data
single-cell
updated 2 days ago by
bk11
★ 2.4k • written 3 days ago by
Kazo
• 0
0
votes
0
replies
154
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 2 days ago by
Ram
43k • written 2 days ago by
SineWave
• 0
0
votes
0
replies
452
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
2 days ago by
biocellbio
• 0
0
votes
5
replies
331
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 1 day ago by
Istvan Albert
100k • written 4 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
100
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
0
replies
105
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
96
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
69
views
adjusting for confounders in LMER in R
confounders
LMER
R
22 hours ago by
rene.j.erhardt
▴ 20
0
votes
1
reply
107
views
Downloading full alignments from Pfam
pfam
updated 14 hours ago by
GenoMax
141k • written 18 hours ago by
bef1
• 0
0
votes
0
replies
10
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
1 hour ago by
Winter
• 0
0
votes
0
replies
12
views
vg call vs vg surject
variation
graphs
1 hour ago by
aliraza3119
• 0
0
votes
0
replies
11
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 40 minutes ago by
Ram
43k • written 47 minutes ago by
WUSCHEL
▴ 750
0
votes
0
replies
70
views
Finding batch and outlayers
Pca
updated 41 minutes ago by
Ram
43k • written 6 hours ago by
Tigran
• 0
0
votes
9
replies
2.4k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 30 minutes ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
0
replies
4
views
Differential accessibility using DiffBinf
diffbind
20 minutes ago by
Shloka
• 0
0
votes
0
replies
133
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 6 days ago by
Carlo Yague
8.7k • written 7 days ago by
Atul K.
• 0
0
votes
0
replies
82
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
6 days ago by
Biostars2200
• 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
6 days ago by
sativus
▴ 20
0
votes
0
replies
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
6 days ago by
Enrique
• 0
0
votes
0
replies
74
views
Imputation advice
imputation
6 days ago by
kl
▴ 10
0
votes
0
replies
85
views
Annotating single cell data automatically
cell
annotation
single
6 days ago by
Gerard
• 0
0
votes
0
replies
86
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
6 days ago by
feather-W
• 0
0
votes
1
reply
157
views
RNA-seq bacteria contamination
RNA-seq
updated 6 days ago by
GenoMax
141k • written 6 days ago by
sh
• 0
0
votes
0
replies
89
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
6 days ago by
manaswwm
▴ 510
0
votes
1
reply
130
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 6 days ago by
ATpoint
82k • written 6 days ago by
enanoide
• 0
0
votes
0
replies
206
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
6 days ago by
Javier
• 0
0
votes
1
reply
139
views
tbtool
tbtool
updated 6 days ago by
Ram
43k • written 6 days ago by
Raman
• 0
0
votes
0
replies
93
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 6 days ago by
Ram
43k • written 6 days ago by
sansan_96
▴ 80
0
votes
0
replies
199
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 6 days ago by
Ram
43k • written 6 days ago by
Oak
▴ 10
84 results • Page
2 of 2
Recent Votes
Comment: PDB related issue
Comment: PDB related issue
Comment: NGS forensics: how to know if data is fabricated
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
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Popular Question
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Zhenyu Zhang
★ 1.2k
Popular Question
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WUSCHEL
▴ 750
Teacher
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Mensur Dlakic
★ 27k
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22k
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Recent Replies
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
I reinstalled nodejs: > sudo apt-get install nodejs Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated
by
Prash
▴ 270
Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 550
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 550
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
Gordon Smyth
★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue
by
noodle
▴ 550
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue
by
Mensur Dlakic
★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
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