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1,000 results • Page
1 of 20
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0
votes
0
replies
20
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
1 hour ago by
sithlordashley
• 0
0
votes
1
reply
28
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 1 hour ago by
GenoMax
140k • written 2 hours ago by
David Tachiquín
• 0
0
votes
5
replies
61
views
Low number of both surviving reads after trimming
trimmomatic
trimming
updated 5 minutes ago by
GenoMax
140k • written 2 hours ago by
Jay
• 0
0
votes
1
reply
47
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
updated 1 hour ago by
GenoMax
140k • written 3 hours ago by
Mohamed Abderrahmane
▴ 10
2
votes
2
replies
62
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
3 hours ago by
DYLAN NICO
• 0
0
votes
0
replies
38
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 3 hours ago by
Ram
43k • written 3 hours ago by
Tolga
▴ 20
0
votes
0
replies
33
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
4 hours ago by
alenew.am
• 0
0
votes
3
replies
235
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
3 hours ago by
Nitin
• 0
0
votes
1
reply
66
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 4 hours ago by
Ram
43k • written 4 hours ago by
chiditatawmbi
• 0
0
votes
1
reply
88
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 4 hours ago by
Ram
43k • written 5 hours ago by
Picasa
▴ 640
0
votes
0
replies
52
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 3 hours ago by
Ram
43k • written 6 hours ago by
udakshi
• 0
0
votes
0
replies
69
views
Training
chip-seq
ScATAC-seq
6 hours ago by
Manhezz
• 0
1
vote
2
replies
90
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 2 hours ago by
Ram
43k • written 7 hours ago by
gdfsnkfns
• 0
1
vote
11
replies
250
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 1 hour ago by
GenoMax
140k • written 7 hours ago by
Lila M
★ 1.2k
2
votes
2
replies
90
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 3 hours ago by
dariober
14k • written 8 hours ago by
Pumla
• 0
0
votes
1
reply
74
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 30 minutes ago by
Ram
43k • written 9 hours ago by
Christian
• 0
0
votes
0
replies
53
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
9 hours ago by
Broccoli
• 0
0
votes
0
replies
51
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
9 hours ago by
blur
▴ 280
0
votes
0
replies
58
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
10 hours ago by
liuyibin2005
• 0
0
votes
0
replies
48
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 4 hours ago by
Ram
43k • written 10 hours ago by
M'zelle
• 0
0
votes
0
replies
66
views
In scRNA, How should I set QC standards?
scRNA
QC
13 hours ago by
mnx0723
• 0
0
votes
0
replies
67
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
16 hours ago by
Chris
▴ 260
2
votes
10
replies
704
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 4 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
0
votes
0
replies
81
views
doing some ontology enrichment analysis
GO
19 hours ago by
aleksk779
• 0
0
votes
2
replies
154
views
novel and know mir156 and mir172
a
updated 18 hours ago by
gayachit
▴ 200 • written 22 hours ago by
Fadmo
• 0
2
votes
8
replies
250
views
Piping samtools to R
R
NGS
bash
samtools
23 hours ago by
joe
▴ 470
0
votes
8
replies
413
views
STAR aligner options
STAR
9 hours ago by
theophile
• 0
0
votes
2
replies
162
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
21 hours ago by
Ankit
▴ 500
0
votes
1
reply
105
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 1 day ago by
Yogi
▴ 70 • written 1 day ago by
Ronin
• 0
0
votes
0
replies
81
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 1 day ago by
Ram
43k • written 1 day ago by
r.shiasi3897
▴ 10
0
votes
0
replies
82
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
1
reply
120
views
How can I remove duplicate SNP?
plink
updated 1 day ago by
iraun
6.2k • written 1 day ago by
Zhennan
• 0
0
votes
1
reply
130
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 1 day ago by
Ram
43k • written 1 day ago by
Hajar
• 0
0
votes
0
replies
76
views
Creating a custom ontology for peptides
ontology
peptide
1 day ago by
Mathew
• 0
0
votes
0
replies
78
views
GSEA number dimension of expression dataset
GSEA
1 day ago by
edoardofilippi1998
• 0
0
votes
0
replies
84
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
0
votes
3
replies
213
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
1 day ago by
sarahmanderni
▴ 100
0
votes
2
replies
152
views
Error with goodSamplesGenes()
R
WGCNA
1 day ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
92
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
7
replies
314
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 19 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
1
reply
142
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
1
reply
138
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 1 day ago by
David Arturo
• 0
0
votes
0
replies
103
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
1 day ago by
kiraqueen
• 0
2
votes
2
replies
210
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
fred.s.kremer
▴ 110
0
votes
0
replies
101
views
Convert VCF file and add covariate information
VCF
PED
PLINK
1 day ago by
asmariyaz23
▴ 10
0
votes
0
replies
99
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 1 day ago by
Ram
43k • written 1 day ago by
hamarillo
▴ 70
2
votes
3
replies
240
views
Extracting information from my VCF file
VCF
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
realtreeecat
• 0
0
votes
4
replies
242
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
7 hours ago by
rohitsatyam102
▴ 840
0
votes
2
replies
270
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 2 days ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
0
votes
0
replies
91
views
How to access an image (slice) of interest in spatial analysis
spatial-transcriptomics
Seurat
Visium
updated 2 days ago by
Ram
43k • written 2 days ago by
piotto
▴ 20
1,000 results • Page
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104k
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Recent Replies
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
A significant fraction of your reads appear to have the nextera sequence, that combined to this directive `LEADING:20` (do you have a reaso…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Here is my fastqc, especially adapter content graph, before trimming(R1 and R2): ![enter image description here][1] And this after trimm…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thanks, I modified.
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Pierre Lindenbaum
160k
11 years ago: https://www.biostars.org/p/7126/
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
haha yes exactly! After the first or second ruined fasta, I started "catting" all fasta files and piping to other commands, just to reduce …
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
... ha, beat me to it, posted at the same time ... this error rules them all .. here is a cool trick on how to count fasta headers in file…
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
I've definitely ruined some genome fasta files by running `grep ^> mygenome.fasta` instead of `grep "^>" mygenome.fasta`
Comment: Error in CIBERSORTx
by
o.nad
• 0
Hello. I faced the same problem but not able to resolve it. I don't have double quotation and no NA values and the dataset used is in the f…
Answer: Annotation of Complex genomes using NCBI Genome Workbench
by
Lissa Cruz Saavedra
• 0
Hi Recently, I used https://www.gensas.org/ to make the annotation. It was pretty practical and in my opinion easy. You just need to up…
Comment: Hybrid assembly Pacbio- Nanopore
by
Lissa Cruz Saavedra
• 0
Hi Thanks for your answer. I think I have very good coverage. My genome size is 48M. I also have data from poreC and illumina, the last on…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Anyone please suggest which variant caller can be the best choice for variant calling of GBS data for polyploid plant.
Comment: Variant calling of GBS data
by
analyst
▴ 10
Does GATK Haplotypecaller take care of ploidy because few plants are polyploid?
Comment: Looking for RPIP Illumina kit probe sequences
by
GenoMax
140k
More than likely they will only be available in the accompanying analysis app (Explify RPIP) in BaseSpace. Check with Illumina tech support…
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Mensur Dlakic
★ 26k
Pretty sure I have done it, but can't remember the details. You know that thing about blocking out traumatic events ...
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by
GenoMax
140k
> I have just noticed in the documentation that there is no argument to specify the number of CPUs to use for calculations. If the program…
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