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181 results • Page
1 of 4
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76
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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 4 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 1 day 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 3 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 1 day ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
8
votes
8
replies
565
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
Aaliya
▴ 10
8
votes
16
replies
840
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 1 day ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
8
votes
5
replies
5.3k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
7
votes
2
replies
267
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 4 days ago by
geneontologyhelp
▴ 390 • written 5 days ago by
catherine.teyssier
• 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 2 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
7
votes
6
replies
481
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
6 days ago by
analyst
▴ 30
6
votes
6
replies
324
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 2 hours ago by
dsull
★ 5.9k • written 5 hours ago by
noodle
▴ 520
6
votes
3
replies
185
views
Interpretting IGV output
IGV
updated 5 days ago by
Carlo Yague
8.7k • written 5 days ago by
analyst
▴ 30
5
votes
3
replies
247
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Estevão
• 0
5
votes
4
replies
636
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
3 days ago by
kirillkirilenko
▴ 40
4
votes
7
replies
557
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 18 hours ago by
dsull
★ 5.9k • written 4 days ago by
qudrat.nii
▴ 10
4
votes
11
replies
597
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 3 days ago by
LauferVA
4.2k • written 4 days ago by
dominickd
• 0
4
votes
2
replies
374
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 2 days ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
4
votes
8
replies
499
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 20 hours ago by
Alex Reynolds
35k • written 1 day ago by
J
▴ 10
4
votes
7
replies
444
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 2 days ago by
dsull
★ 5.9k • written 3 days ago by
VITALA
• 0
4
votes
4
replies
371
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 11 hours ago by
BioinfGuru
★ 1.7k • written 2 days ago by
Ming Tommy Tang
★ 3.9k
3
votes
3
replies
226
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 5 days ago by
GenoMax
141k • written 5 days ago by
Mariana
▴ 10
3
votes
5
replies
554
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
5 days ago by
n_navy
• 0
3
votes
3
replies
720
views
KissDE and batch effect
kissDE
kissplice
5 days ago by
david.b.rombaut
▴ 10
3
votes
9
replies
449
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 3 days ago by
Istvan Albert
100k • written 5 days ago by
Κοσμάς
• 0
3
votes
5
replies
275
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 5 days ago by
GenoMax
141k • written 5 days ago by
ahmad.sajad4541
• 0
3
votes
3
replies
227
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
M
• 0
3
votes
3
replies
204
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sapuizait
▴ 10
3
votes
4
replies
283
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
2 days ago by
QX
• 0
3
votes
6
replies
655
views
Ciriquant not configuring hisat2 indexed files
ciriquant
5 days ago by
Atul K.
• 0
3
votes
1
reply
222
views
Seurat merge and batch correction
Seurat
updated 4 days ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
3
votes
3
replies
200
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
c_u
▴ 520
3
votes
0
replies
122
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 4 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 2 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
0
replies
128
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 1 day ago by
Ram
43k • written 1 day ago by
Claire Watson
▴ 60
3
votes
4
replies
666
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
5 days ago by
rahu
• 0
3
votes
2
replies
276
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
5 days ago by
kristiewyleung
• 0
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 1 day ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
2
votes
3
replies
950
views
Method to detect genome doubling
CNV
genome doubling
updated 5 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
2
votes
4
replies
2.4k
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 2 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
2
votes
3
replies
204
views
from row count to tpm
tpm
row-count
normalization
4 days ago by
michelafrancesconi9
▴ 20
2
votes
4
replies
279
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
3 days ago by
samuelkalandarov2002
▴ 10
2
votes
2
replies
233
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 1 day ago by
dsull
★ 5.9k • written 1 day ago by
Aaliya
▴ 10
2
votes
3
replies
328
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 1 day ago by
dsull
★ 5.9k • written 18 days ago by
javanokendo
▴ 60
2
votes
4
replies
295
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 2 days ago by
Ram
43k • written 2 days ago by
ashaneev07
▴ 20
2
votes
4
replies
316
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
9
replies
842
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 3 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
2
replies
213
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 3 days ago by
analyst
▴ 30 • written 4 days ago by
lorena9132
• 0
2
votes
3
replies
307
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
emmanouil.a
▴ 120
2
votes
4
replies
306
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
dxj294
• 0
181 results • Page
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Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
correcting for a batch in DESeq2
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Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
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> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
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Francesco
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Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
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> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
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This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
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[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
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Use the standalone version of Nextflow and specify the process-specific conda environments paths.
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Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
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just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
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Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
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