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185 results • Page
1 of 4
Sort: 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
3 days ago by
Kevin Blighe
87k
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 5 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 2 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
15
votes
12
replies
764
views
7 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 58 minutes ago by
benformatics
3.9k • written 1 day ago by
noodle
▴ 530
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 4 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 2 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
8
votes
16
replies
880
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 2 days ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
8
votes
8
replies
585
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 3 days ago by
swbarnes2
14k • written 4 days ago by
Aaliya
▴ 10
8
votes
5
replies
5.4k
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 3 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
7
votes
2
replies
273
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 5 days ago by
geneontologyhelp
▴ 390 • written 6 days ago by
catherine.teyssier
• 0
6
votes
3
replies
186
views
Interpretting IGV output
IGV
updated 6 days ago by
Carlo Yague
8.7k • written 6 days ago by
analyst
▴ 30
5
votes
4
replies
642
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
4 days ago by
kirillkirilenko
▴ 40
5
votes
3
replies
257
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 5 days ago by
GenoMax
141k • written 5 days ago by
Estevão
• 0
4
votes
7
replies
462
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 3 days ago by
dsull
★ 5.9k • written 4 days ago by
VITALA
• 0
4
votes
2
replies
378
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
11
replies
694
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 4 days ago by
LauferVA
4.2k • written 5 days ago by
dominickd
• 0
4
votes
8
replies
555
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 1 day ago by
Alex Reynolds
35k • written 2 days ago by
J
▴ 10
4
votes
4
replies
389
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 1 day ago by
BioinfGuru
★ 1.7k • written 3 days ago by
Ming Tommy Tang
★ 3.9k
4
votes
7
replies
612
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 1 day ago by
dsull
★ 5.9k • written 5 days ago by
qudrat.nii
▴ 10
3
votes
4
replies
670
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
6 days ago by
rahu
• 0
3
votes
2
replies
278
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
6 days ago by
kristiewyleung
• 0
3
votes
3
replies
246
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sapuizait
▴ 10
3
votes
3
replies
232
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 6 days ago by
GenoMax
141k • written 6 days ago by
Mariana
▴ 10
3
votes
0
replies
166
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 2 days ago by
Ram
43k • written 2 days ago by
Claire Watson
▴ 60
3
votes
1
reply
224
views
Seurat merge and batch correction
Seurat
updated 5 days ago by
Ram
43k • written 5 days ago by
sooni
▴ 20
3
votes
3
replies
268
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 3 days ago by
swbarnes2
14k • written 3 days ago by
M
• 0
3
votes
9
replies
463
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 4 days ago by
Istvan Albert
100k • written 6 days ago by
Κοσμάς
• 0
3
votes
3
replies
722
views
KissDE and batch effect
kissDE
kissplice
6 days ago by
david.b.rombaut
▴ 10
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 3 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
6
replies
662
views
Ciriquant not configuring hisat2 indexed files
ciriquant
6 days ago by
Atul K.
• 0
3
votes
3
replies
204
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 6 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
c_u
▴ 520
3
votes
0
replies
123
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 5 days ago by
Ram
43k • written 5 days ago by
carlopecoraro2
★ 2.5k
3
votes
4
replies
322
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
3 days ago by
QX
• 0
3
votes
5
replies
556
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
6 days ago by
n_navy
• 0
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 2 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
3
votes
5
replies
279
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 6 days ago by
GenoMax
141k • written 6 days ago by
ahmad.sajad4541
• 0
2
votes
3
replies
332
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 2 days ago by
dsull
★ 5.9k • written 19 days ago by
javanokendo
▴ 60
2
votes
1
reply
221
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 3 days ago by
Adrian Altenhoff
★ 1.1k • written 4 days ago by
hemantcnaik
• 0
2
votes
5
replies
459
views
Marking duplicates using UMIs
Deduplication
UMI
updated 6 days ago by
i.sudbery
19k • written 8 days ago by
Lipika
• 0
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 3 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
2
votes
3
replies
956
views
Method to detect genome doubling
CNV
genome doubling
updated 6 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 3 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
2
votes
2
replies
221
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 4 days ago by
analyst
▴ 30 • written 5 days ago by
lorena9132
• 0
2
votes
5
replies
308
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
2 days ago by
Lada
▴ 30
2
votes
4
replies
322
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
4 days ago by
HyperEvo
• 0
2
votes
3
replies
210
views
from row count to tpm
tpm
row-count
normalization
5 days ago by
michelafrancesconi9
▴ 20
2
votes
4
replies
311
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
dxj294
• 0
2
votes
9
replies
846
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 4 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
3
replies
316
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 6 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
emmanouil.a
▴ 120
185 results • Page
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Recent Votes
Comment: NGS forensics: how to know if data is fabricated
A: Hard time trying to calculate Allele Frequency and DP from Platypus
Answer: 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
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Answer: Finding batch and outlayers
by
Tigran
• 0
![enter image description here][1] [1]: /media/images/aa60b9ef-b08c-4093-9f0d-fb656a5c
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue
by
noodle
▴ 530
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue
by
Mensur Dlakic
★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I think you might be getting stuck on less relevant parts of my exercise. The most important point was that nothing is wrong with the data.…
Comment: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
Comment: Cannot process all the reads in a fast5 file?
by
chujie
• 0
Hi, I met the same problem, have you found the solution?
Answer: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
Hi @fe3e6f65 , In a single sentence, the answer to your question can be summarized as, "*the resolution of a genomic technology refers to …
Comment: PCA plot
by
LauferVA
4.2k
Without more context, we cannot interpret this PCA plot. There are many possibilities. In addition, this question is basic enough that it w…
Comment: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
i have the name ready: out**liar**
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