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83 results • Page
1 of 2
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0
votes
0
replies
2
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
just now by
DOBI
• 0
0
votes
0
replies
7
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
20 minutes ago by
Ruqaiya
• 0
0
votes
0
replies
9
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
30 minutes ago by
atharvakarkare14
▴ 10
0
votes
0
replies
15
views
What should I consider as FASTA for dataset?
PDB
FASTA
52 minutes ago by
Nafi
• 0
0
votes
0
replies
15
views
Differential accessibility using DiffBinf
diffbind
2 hours ago by
Shloka
• 0
0
votes
0
replies
26
views
vg call vs vg surject
variation
graphs
3 hours ago by
aliraza3119
• 0
0
votes
0
replies
24
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
3 hours ago by
Winter
• 0
0
votes
0
replies
85
views
Finding batch and outlayers
Pca
updated 2 hours ago by
Ram
43k • written 8 hours ago by
Tigran
• 0
2
votes
2
replies
133
views
PDB related issue
rcsb
pdb
updated 8 hours ago by
noodle
▴ 560 • written 11 hours ago by
Nafi
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 2 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
1
reply
110
views
Downloading full alignments from Pfam
pfam
updated 16 hours ago by
GenoMax
141k • written 20 hours ago by
bef1
• 0
0
votes
0
replies
73
views
adjusting for confounders in LMER in R
confounders
LMER
R
1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
230
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 14 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
99
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
111
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
104
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
0
replies
463
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
0
replies
182
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
2 days ago by
HarperReed
• 0
1
vote
0
replies
142
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
3 days ago by
KABILAN
▴ 50
0
votes
0
replies
159
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 2 days ago by
Ram
43k • written 3 days ago by
SineWave
• 0
0
votes
0
replies
152
views
RNA-seq: full length gene
RNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
Nargis
• 0
0
votes
0
replies
144
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
3 days ago by
turcoa1
• 0
0
votes
0
replies
153
views
Designing single-stable RNA molecules
structure
RNA
3 days ago by
Edna
• 0
0
votes
0
replies
168
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
3 days ago by
simplitia
▴ 130
0
votes
1
reply
207
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 3 days ago by
ATpoint
82k • written 3 days ago by
AaronJaime
• 0
0
votes
0
replies
162
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
3 days ago by
avocado123
• 0
0
votes
0
replies
149
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
3 days ago by
Emily
▴ 10
1
vote
0
replies
162
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
3 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
148
views
how to read graph_test output of monocle 3
monocle3
3 days ago by
synat.keam
▴ 100
0
votes
1
reply
477
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 3 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
146
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
3 days ago by
Aspire
▴ 300
0
votes
3
replies
277
views
Highest variable features in single cell data
single-cell
updated 2 days ago by
bk11
★ 2.4k • written 4 days ago by
Kazo
• 0
1
vote
3
replies
328
views
PCA plot
DESeq2
PCAplot
updated 13 hours ago by
LauferVA
4.2k • written 4 days ago by
Aaliya
▴ 10
0
votes
0
replies
144
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
4 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
245
views
Annovar using R package
Annovar
gnomAD
R
3 days ago by
DKA
▴ 40
0
votes
5
replies
334
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 3 days ago by
GenoMax
141k • written 4 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
137
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 4 days ago by
Ram
43k • written 4 days ago by
glaciya2018
• 0
0
votes
0
replies
304
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
4 days ago by
pramach1
▴ 40
0
votes
1
reply
153
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 4 days ago by
Sofia
• 0 • written 4 days ago by
mawigoj318
• 0
0
votes
0
replies
139
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
4 days ago by
salias
• 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
119
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 4 days ago by
Ram
43k • written 4 days ago by
newuser2024
• 0
1
vote
2
replies
224
views
alignment result
RNA-seq
samtools
hisat2
4 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
102
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 4 days ago by
Ram
43k • written 5 days ago by
Jeyong
• 0
0
votes
0
replies
110
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
5 days ago by
Kash
▴ 110
0
votes
1
reply
154
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
251
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 4 days ago by
Ram
43k • written 5 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
847
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 5 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
524
views
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
1
reply
162
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 5 days ago by
bk11
★ 2.4k • written 5 days ago by
alphaflylizard
• 0
83 results • Page
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Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
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Comment: NGS forensics: how to know if data is fabricated
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Comment: What does it mean single base resolution in sequencing?
by
jinyu
▴ 10
Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
Answer: Is it possible to bulk download files from GEO repository?
by
atharvakarkare14
▴ 10
Try using this library [GEOparse][1] [1]: https://github.com/guma44/GEOparse
Answer: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
OK. Problem solved. The problem was from my end. Thank you both for helping !!
Comment: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
Appreciate the suggestion, but that ship has sailed and reached the other shore. This happened 10+ years ago. To the best of my knowledge n…
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by
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▴ 30
Files are not opening in any of the computer (ubuntu/windows). I rereun snpEff annotation but still output html files are having missing im…
Comment: Figures are disappeared from html report of SnpEff
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analyst
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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
▴ 280
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
▴ 560
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
▴ 560
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 …
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> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
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