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195 results • Page
1 of 4
Sort: Votes
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Votes
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76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
19 hours ago by
Kevin Blighe
87k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 6 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 2 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 23 hours ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
11
votes
12
replies
939
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 6 days ago by
Ram
43k • written 7 days ago by
iamsmor
• 0
8
votes
5
replies
5.0k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 5 hours ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 6 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
7
votes
2
replies
254
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 3 days ago by
catherine.teyssier
• 0
7
votes
6
replies
460
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
4 days ago by
analyst
▴ 30
6
votes
3
replies
170
views
Interpretting IGV output
IGV
updated 3 days ago by
Carlo Yague
8.7k • written 3 days ago by
analyst
▴ 30
5
votes
3
replies
704
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 6 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 5 days ago by
ATpoint
82k • written 6 days ago by
BioinfGuru
★ 1.7k
5
votes
4
replies
619
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
1 day ago by
kirillkirilenko
▴ 40
4
votes
11
replies
495
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 1 day ago by
LauferVA
4.2k • written 2 days ago by
dominickd
• 0
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
4
votes
7
replies
389
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 13 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
3
votes
3
replies
713
views
KissDE and batch effect
kissDE
kissplice
3 days ago by
david.b.rombaut
▴ 10
3
votes
13
replies
644
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 1 day ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 0
3
votes
5
replies
252
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 3 days ago by
GenoMax
141k • written 3 days ago by
ahmad.sajad4541
• 0
3
votes
2
replies
266
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
3 days ago by
kristiewyleung
• 0
3
votes
9
replies
407
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 1 day ago by
Istvan Albert
100k • written 3 days ago by
Κοσμάς
• 0
3
votes
6
replies
641
views
Ciriquant not configuring hisat2 indexed files
ciriquant
3 days ago by
Atul K.
• 0
3
votes
4
replies
650
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
3 days ago by
rahu
• 0
3
votes
3
replies
189
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
c_u
▴ 520
3
votes
4
replies
160
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
2 hours ago by
QX
• 0
3
votes
3
replies
207
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Mariana
▴ 10
3
votes
3
replies
501
views
Korean human genome reference file
GWAS
reference
imputation
6 days ago by
SeoGyun
• 0
3
votes
0
replies
110
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
3
votes
8
replies
463
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 16 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
3
votes
5
replies
538
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
3 days ago by
n_navy
• 0
3
votes
3
replies
211
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Estevão
• 0
3
votes
3
replies
466
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
joe
▴ 510
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 5 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 7 hours ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
2
votes
4
replies
240
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 1 day ago by
GenoMax
141k • written 2 days ago by
Lada
▴ 30
2
votes
1
reply
285
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 5 days ago by
GenoMax
141k • written 6 days ago by
rebecca.calvo
• 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 6 days ago by
ATpoint
82k • written 7.2 years ago by
boymin2020
▴ 80
2
votes
2
replies
413
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 2 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
2
votes
7
replies
811
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 8 days ago by
quentinperriere
• 0
2
votes
4
replies
252
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
1 day ago by
samuelkalandarov2002
▴ 10
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 17 hours ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
2
votes
3
replies
261
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
emmanouil.a
▴ 120
2
votes
1
reply
199
views
Seurat merge and batch correction
Seurat
updated 2 days ago by
Ram
43k • written 2 days ago by
sooni
▴ 20
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 4 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
2
votes
9
replies
814
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
3
replies
311
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 3 days ago by
dsull
★ 5.8k • written 16 days ago by
javanokendo
▴ 60
2
votes
5
replies
516
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 4 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
Giorgio
• 0
2
votes
3
replies
189
views
from row count to tpm
tpm
row-count
normalization
2 days ago by
michelafrancesconi9
▴ 20
2
votes
4
replies
280
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
1 day ago by
HyperEvo
• 0
195 results • Page
1 of 4
Recent Votes
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package
by
DKA
▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
ATpoint
82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
Bioinfotec
▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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