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187 results • Page
2 of 4
Sort: Rank
Rank
Views
Votes
Replies
8
votes
8
replies
539
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
772
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
915
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
2 days ago by
DKA
▴ 40
0
votes
2
replies
798
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
292
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
130
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
112
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
264
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
141
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
132
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
2 days ago by
salias
• 0
4
votes
7
replies
418
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
250
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
113
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
202
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
109
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
94
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
215
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
203
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 2 days ago by
analyst
▴ 30 • written 2 days ago by
lorena9132
• 0
0
votes
0
replies
105
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
2 days ago by
Kash
▴ 110
7
votes
2
replies
263
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 2 days ago by
geneontologyhelp
▴ 390 • written 4 days ago by
catherine.teyssier
• 0
1
vote
1
reply
202
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 2 days ago by
Istvan Albert
100k • written 4 days ago by
Abeer
• 0
2
votes
4
replies
293
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 2 days ago by
swbarnes2
14k • written 4 days ago by
dxj294
• 0
0
votes
1
reply
147
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
238
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
219
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
184
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
144
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
823
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
477
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
21 hours ago by
atowns21
• 0
0
votes
1
reply
153
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
228
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
236
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 2 days ago by
Istvan Albert
100k • written 3 days ago by
Dylan
• 0
2
votes
5
replies
279
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
13 hours ago by
Lada
▴ 30
4
votes
11
replies
524
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 2 days ago by
LauferVA
4.2k • written 3 days ago by
dominickd
• 0
8
votes
16
replies
788
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 5 hours ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
0
votes
0
replies
94
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
3 days ago by
ohtang7
▴ 40
3
votes
0
replies
117
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
419
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
156
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
298
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
625
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
2 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
88
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
370
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
210
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
209
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
vote
1
reply
156
views
WGCNA preservation analysis
WGCNA
preservation
updated 3 days ago by
Michael
54k • written 3 days ago by
michael.flower.14
▴ 180
1
vote
3
replies
250
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
187 results • Page
2 of 4
Recent Votes
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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Recent Replies
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 :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
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