Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
227
views
Annovar using R package
Annovar
gnomAD
R
1 day ago by
DKA
▴ 40
0
votes
2
replies
211
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
biochugs
• 0
8
votes
8
replies
546
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
Aaliya
▴ 10
1
vote
8
replies
777
views
Adding CB tag to bam file
samtools
bam
updated 1 day ago by
Pierre Lindenbaum
161k • written 8 days ago by
Maria
• 0
1
vote
10
replies
918
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
2 days ago by
DKA
▴ 40
0
votes
2
replies
801
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 2 days ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
296
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 1 day ago by
GenoMax
141k • written 2 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
131
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 2 days ago by
Ram
43k • written 2 days ago by
glaciya2018
• 0
0
votes
0
replies
113
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 1 day ago by
Ram
43k • written 2 days ago by
David Langenberger
11k
0
votes
0
replies
269
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
2 days ago by
pramach1
▴ 40
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 2 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
143
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 2 days ago by
Sofia
• 0 • written 2 days ago by
mawigoj318
• 0
0
votes
0
replies
134
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
2 days ago by
salias
• 0
4
votes
7
replies
421
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 1 day ago by
dsull
★ 5.8k • written 2 days ago by
VITALA
• 0
0
votes
4
replies
254
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
114
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 2 days ago by
Ram
43k • written 2 days ago by
newuser2024
• 0
1
vote
2
replies
204
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
110
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
97
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 2 days ago by
Ram
43k • written 2 days ago by
Jeyong
• 0
0
votes
2
replies
218
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
2 days ago by
mropri
▴ 150
2
votes
2
replies
206
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 2 days ago by
analyst
▴ 30 • written 3 days ago by
lorena9132
• 0
0
votes
0
replies
106
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
3 days ago by
Kash
▴ 110
7
votes
2
replies
264
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 3 days ago by
geneontologyhelp
▴ 390 • written 4 days ago by
catherine.teyssier
• 0
1
vote
1
reply
205
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 3 days ago by
Istvan Albert
100k • written 4 days ago by
Abeer
• 0
2
votes
4
replies
296
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 3 days ago by
swbarnes2
14k • written 4 days ago by
dxj294
• 0
0
votes
1
reply
149
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
239
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 2 days ago by
Ram
43k • written 3 days ago by
v.berriosfarias
▴ 140
3
votes
1
reply
220
views
Seurat merge and batch correction
Seurat
updated 3 days ago by
Ram
43k • written 3 days ago by
sooni
▴ 20
1
vote
1
reply
186
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Biostar
2.7k
1
vote
1
reply
147
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 3 days ago by
GenoMax
141k • written 3 days ago by
heelpPlease
• 0
2
votes
9
replies
826
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 3 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
486
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
0
votes
1
reply
156
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
alphaflylizard
• 0
5
votes
3
replies
236
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Estevão
• 0
0
votes
3
replies
243
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 3 days ago by
Istvan Albert
100k • written 3 days ago by
Dylan
• 0
2
votes
5
replies
282
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
19 hours ago by
Lada
▴ 30
4
votes
11
replies
527
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 3 days ago by
LauferVA
4.2k • written 4 days ago by
dominickd
• 0
8
votes
16
replies
814
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 11 hours ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
0
votes
0
replies
97
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
3 days ago by
ohtang7
▴ 40
3
votes
0
replies
118
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
424
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 3 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
157
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Srinka
▴ 20
8
votes
5
replies
5.2k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
5
replies
300
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
2 days ago by
njornet
▴ 20
5
votes
4
replies
626
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
2 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
90
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 3 days ago by
Ram
43k • written 3 days ago by
SHREYA
• 0
0
votes
3
replies
372
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 3 days ago by
colindaven
6.4k • written 11 days ago by
rj.rezwan
• 0
0
votes
0
replies
97
views
Merging replicates from Encode project
CHIP-seq
encode
3 days ago by
Nurken
• 0
1
vote
3
replies
216
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
0
votes
3
replies
211
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 3 days ago by
mchour
• 0 • written 3 days ago by
rhossen
• 0
1,000 results • Page
2 of 20
Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
Recent Locations •
All
Chile,
3 minutes ago
Australia,
4 minutes ago
United States,
30 minutes ago
United States,
40 minutes ago
USA,
54 minutes ago
United States,
56 minutes ago
United Kingdom,
59 minutes ago
Recent Awards •
All
Scholar
to
Alex Reynolds
35k
Popular Question
to
chaco001
▴ 40
Commentator
to
GenoMax
141k
Popular Question
to
rheab1230
▴ 140
Popular Question
to
BioinfGuru
★ 1.7k
Scholar
to
bk11
★ 2.4k
Popular Question
to
vinayjrao
▴ 250
Recent Replies
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Traffic: 1806 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6