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13,537 results • Page
3 of 271
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
250
views
Annovar using R package
Annovar
gnomAD
R
4 days ago by
DKA
▴ 40
0
votes
2
replies
230
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
biochugs
• 0
8
votes
8
replies
597
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
Aaliya
▴ 10
1
vote
8
replies
823
views
Adding CB tag to bam file
samtools
bam
updated 4 days ago by
Pierre Lindenbaum
161k • written 11 days ago by
Maria
• 0
1
vote
10
replies
952
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
5 days ago by
DKA
▴ 40
0
votes
2
replies
815
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 5 days ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
339
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 4 days ago by
GenoMax
141k • written 5 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
139
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 5 days ago by
Ram
43k • written 5 days ago by
glaciya2018
• 0
0
votes
0
replies
119
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 4 days ago by
Ram
43k • written 5 days ago by
David Langenberger
11k
0
votes
0
replies
306
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
5 days ago by
pramach1
▴ 40
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 5 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
155
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 5 days ago by
Sofia
• 0 • written 5 days ago by
mawigoj318
• 0
0
votes
0
replies
141
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
5 days ago by
salias
• 0
4
votes
7
replies
468
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 4 days ago by
dsull
★ 5.9k • written 5 days ago by
VITALA
• 0
0
votes
5
replies
336
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 2 days ago by
Istvan Albert
100k • written 5 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
121
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 5 days ago by
Ram
43k • written 5 days ago by
newuser2024
• 0
1
vote
2
replies
231
views
alignment result
RNA-seq
samtools
hisat2
4 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
117
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 5 days ago by
Ram
43k • written 5 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
103
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 5 days ago by
Ram
43k • written 5 days ago by
Jeyong
• 0
0
votes
2
replies
230
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
5 days ago by
mropri
▴ 150
2
votes
2
replies
227
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 5 days ago by
analyst
▴ 30 • written 6 days ago by
lorena9132
• 0
0
votes
0
replies
111
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
6 days ago by
Kash
▴ 110
7
votes
2
replies
275
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 6 days ago by
geneontologyhelp
▴ 390 • written 7 days ago by
catherine.teyssier
• 0
1
vote
1
reply
214
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 6 days ago by
Istvan Albert
100k • written 7 days ago by
Abeer
• 0
2
votes
4
replies
317
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
dxj294
• 0
0
votes
1
reply
156
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 5 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
266
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 5 days ago by
Ram
43k • written 6 days ago by
v.berriosfarias
▴ 140
3
votes
1
reply
226
views
Seurat merge and batch correction
Seurat
updated 6 days ago by
Ram
43k • written 6 days ago by
sooni
▴ 20
1
vote
1
reply
199
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
Biostar
2.7k
1
vote
1
reply
153
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 6 days ago by
GenoMax
141k • written 6 days ago by
heelpPlease
• 0
2
votes
9
replies
851
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
532
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
4 days ago by
atowns21
• 0
0
votes
1
reply
164
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 6 days ago by
bk11
★ 2.4k • written 6 days ago by
alphaflylizard
• 0
5
votes
3
replies
273
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 6 days ago by
GenoMax
141k • written 6 days ago by
Estevão
• 0
0
votes
3
replies
256
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 6 days ago by
Istvan Albert
100k • written 6 days ago by
Dylan
• 0
2
votes
5
replies
319
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
3 days ago by
Lada
▴ 30
4
votes
11
replies
728
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 5 days ago by
LauferVA
4.2k • written 6 days ago by
dominickd
• 0
8
votes
16
replies
903
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 3 days ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
0
votes
0
replies
101
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
6 days ago by
ohtang7
▴ 40
3
votes
0
replies
125
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 6 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
436
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 6 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
167
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 6 days ago by
GenoMax
141k • written 6 days ago by
Srinka
▴ 20
8
votes
5
replies
5.5k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
5
replies
325
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
5 days ago by
njornet
▴ 20
5
votes
4
replies
649
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
5 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
95
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 6 days ago by
Ram
43k • written 6 days ago by
SHREYA
• 0
0
votes
3
replies
395
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 6 days ago by
colindaven
6.4k • written 14 days ago by
rj.rezwan
• 0
0
votes
0
replies
102
views
Merging replicates from Encode project
CHIP-seq
encode
6 days ago by
Nurken
• 0
1
vote
3
replies
235
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
6 days ago by
WouterDeCoster
47k
0
votes
3
replies
228
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 6 days ago by
mchour
• 0 • written 6 days ago by
rhossen
• 0
13,537 results • Page
3 of 271
Recent Votes
Comment: High Malat-1 expression in single cell data
Answer: Extract protein sequence
Answer: Extract protein sequence
C: How do I ask a question on Biostars?
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
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Answer: Why cd-hit-est not work when sequence identity threshold<0.95?
by
weidonglu
• 0
The reason for your problem was most likely due to you relative complex data and too little system memory. For 20000-30000 transcriptome se…
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴ 80
Your table should look like this (GO terms): ``` geneid GOid Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739 Zm00001eb000020 G…
Answer: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴ 80
I understand, here is an example with topGO where you need a differential expression table (DESeq2 for example) and a table of GO terms: `…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
Hamtaro
▴ 50
Thank u for your reply. The problem is that I used the genome and gene annotation from that webpage, not ensemble or ncbi, so I have to use…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
sansan_96
▴ 80
Hello, To perform functional enrichment analysis there are packages such as topGO or clusterProfiler that can work very well. Lately I've …
Answer: Post-imputation plot
by
LChart
3.9k
The anti-diagonal band does suggest some fraction of genotypes are strand-flipped - probably G/C or A/T variants.
Comment: Differential Accessibility
by
Ram
43k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: Extract protein sequence
by
anna
▴ 20
Thank you! I need this for eukaryotic organism and known protein sequences, but I guess seqkit would work well!
Comment: Landmark gene selection in L1000.
by
GenoMax
141k
Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/ > so I want to understand how you reduced the 12063 genes to 978…
Comment: What should I consider as FASTA for dataset?
by
Nafi
• 0
Protein attribute prediction
Comment: Batch effects : ComBat or removebatcheffects (limma package) ?
by
cwwong13
▴ 40
@kevin May I know whether your comments and edits were mainly based on the fact that "Previously, [crazy] people had been using the origina…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 570
> Can you clarify what you mean by "100% of reads pass cutadapt, even > though 70% of reads contain adapters and get trimmed. The header o…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
by
Matthias Zepper
4.5k
You didn't mention what kind of organism you are working with and what kind of protein you are looking for? If it happens to be a microbia…
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