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188 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
2 days ago by
Kevin Blighe
87k
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 3 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 12 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 2 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 17 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
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
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
8
votes
5
replies
5.2k
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 1 day ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
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
7
votes
6
replies
474
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
5 days ago by
analyst
▴ 30
6
votes
3
replies
182
views
Interpretting IGV output
IGV
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
analyst
▴ 30
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
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 6 days ago by
ATpoint
82k • written 7 days ago by
BioinfGuru
★ 1.7k
5
votes
4
replies
626
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
2 days ago by
kirillkirilenko
▴ 40
4
votes
8
replies
377
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
4 hours ago by
J
▴ 10
4
votes
2
replies
370
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 1 day ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
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
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
3
votes
3
replies
222
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Mariana
▴ 10
3
votes
3
replies
198
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
M
• 0
3
votes
4
replies
657
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
4 days ago by
rahu
• 0
3
votes
4
replies
249
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
1 day ago by
QX
• 0
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 6 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
3
votes
0
replies
99
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 6 hours ago by
Ram
43k • written 17 hours ago by
Claire Watson
▴ 60
3
votes
5
replies
547
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
4 days ago by
n_navy
• 0
3
votes
2
replies
273
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
4 days ago by
kristiewyleung
• 0
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
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 1 day ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
6
replies
650
views
Ciriquant not configuring hisat2 indexed files
ciriquant
4 days ago by
Atul K.
• 0
3
votes
3
replies
719
views
KissDE and batch effect
kissDE
kissplice
4 days ago by
david.b.rombaut
▴ 10
3
votes
6
replies
433
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 6 hours ago by
GenoMax
141k • written 3 days ago by
qudrat.nii
▴ 10
3
votes
5
replies
267
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 4 days ago by
GenoMax
141k • written 4 days ago by
ahmad.sajad4541
• 0
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
3
votes
3
replies
195
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
c_u
▴ 520
3
votes
3
replies
471
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
3
votes
9
replies
432
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 2 days ago by
Istvan Albert
100k • written 4 days ago by
Κοσμάς
• 0
3
votes
3
replies
171
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 15 hours ago by
GenoMax
141k • written 18 hours ago by
sapuizait
▴ 10
2
votes
5
replies
452
views
Marking duplicates using UMIs
Deduplication
UMI
updated 4 days ago by
i.sudbery
19k • written 6 days ago by
Lipika
• 0
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 5 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
2
votes
4
replies
304
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
3 days ago by
HyperEvo
• 0
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 1 day ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
2
votes
4
replies
250
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 1 day ago by
Ram
43k • written 1 day ago by
ashaneev07
▴ 20
2
votes
5
replies
522
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 6 days ago by
Mensur Dlakic
★ 27k • written 7 days ago by
Giorgio
• 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
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
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
2
votes
1
reply
172
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 1 day ago by
Adrian Altenhoff
★ 1.1k • written 2 days ago by
hemantcnaik
• 0
2
votes
3
replies
214
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
analyst
▴ 30
2
votes
3
replies
948
views
Method to detect genome doubling
CNV
genome doubling
updated 4 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
188 results • Page
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Recent Votes
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A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
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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
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Recent Replies
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
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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
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Gordon Smyth
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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
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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…
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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141k
Please include a link when you are recommending a tool. There can be programs with similar names.
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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…
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You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
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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)…
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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…
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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 :(
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