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1,000 results • Page
1 of 20
Sort: Rank
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14
votes
10
replies
728
views
6 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 2 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
noodle
▴ 530
0
votes
1
reply
43
views
PDB related issue
rcsb
pdb
updated 50 minutes ago by
Mensur Dlakic
★ 27k • written 2 hours ago by
Nafi
• 0
0
votes
0
replies
33
views
News:
Online course: Genome Annotation
GenomeAssembly
GenomeAnnoration
4 hours ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
135
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 3 hours ago by
dsull
★ 5.9k • written 4 hours ago by
jinyu
▴ 10
0
votes
9
replies
2.4k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
nanopore
basecalling
fastq
updated 4 hours ago by
chujie
• 0 • written 8 months ago by
Gio
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
2
votes
5
replies
358
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
4 hours ago by
ashaneev07
▴ 20
0
votes
1
reply
89
views
Downloading full alignments from Pfam
pfam
updated 7 hours ago by
GenoMax
141k • written 11 hours ago by
bef1
• 0
0
votes
1
reply
689
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 11 hours ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
1
vote
1
reply
180
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 1 hour ago by
ATpoint
82k • written 2 days ago by
vanbelj
▴ 40
2
votes
6
replies
1.1k
views
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 14 hours ago by
Ram
43k • written 8 months ago by
Calum
▴ 10
0
votes
0
replies
58
views
adjusting for confounders in LMER in R
confounders
LMER
R
16 hours ago by
rene.j.erhardt
▴ 20
0
votes
12
replies
348
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
updated 2 hours ago by
Mensur Dlakic
★ 27k • written 20 hours ago by
Ruqaiya
• 0
1
vote
3
replies
205
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 5 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
88
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
95
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
91
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
1
reply
277
views
absolute path for symbolic links in Snakefile
Snakemake
updated 1 day ago by
Jesse
▴ 740 • written 9 days ago by
yifangt86
▴ 60
0
votes
2
replies
289
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 1 day ago by
Jesse
▴ 740 • written 3 days ago by
Broccoli
• 0
2
votes
3
replies
273
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 1 day ago by
Arup Ghosh
3.2k • written 2 days ago by
chaco001
▴ 40
1
vote
3
replies
307
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 2 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
O.rka
▴ 710
0
votes
1
reply
180
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 2 days ago by
hagl
▴ 10
0
votes
2
replies
212
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
1 day ago by
Guille
• 0
2
votes
1
reply
177
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 2 days ago by
pairedttest
▴ 10
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
0
votes
0
replies
413
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
2 days ago by
biocellbio
• 0
4
votes
8
replies
550
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
7
replies
611
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
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
2
votes
2
replies
277
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 2 days ago by
dsull
★ 5.9k • written 2 days ago by
Aaliya
▴ 10
3
votes
0
replies
165
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
0
votes
2
replies
237
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 2 days ago by
Ram
43k • written 3 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
170
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
2 days ago by
HarperReed
• 0
3
votes
3
replies
245
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
1
vote
0
replies
131
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
2 days ago by
KABILAN
▴ 50
0
votes
0
replies
145
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 2 days ago by
Ram
43k • written 2 days ago by
SineWave
• 0
0
votes
0
replies
138
views
RNA-seq: full length gene
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Nargis
• 0
1
vote
7
replies
403
views
gvcf joint calling
WES
GATK
VCF
gVCF
14 hours ago by
zihanss
• 0
0
votes
0
replies
130
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
2 days ago by
turcoa1
• 0
3
votes
3
replies
266
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
0
votes
0
replies
142
views
Designing single-stable RNA molecules
structure
RNA
3 days ago by
Edna
• 0
0
votes
0
replies
156
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
3 days ago by
simplitia
▴ 130
0
votes
1
reply
193
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 3 days ago by
ATpoint
82k • written 3 days ago by
AaronJaime
• 0
0
votes
2
replies
256
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
288
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
293
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
1 day ago by
Francesco
▴ 10
1
vote
6
replies
395
views
ScRNA data question
scRNA
Vlnplot
Samples
1 day ago by
starswillfade
▴ 10
0
votes
0
replies
155
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
3 days ago by
avocado123
• 0
0
votes
0
replies
149
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
149
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
3 days ago by
Emily
▴ 10
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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
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
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**
Comment: What does it mean single base resolution in sequencing?
by
GenoMax
141k
Sequencing by hybridization (https://en.wikipedia.org/wiki/Sequencing_by_hybridization ) is likely not giving you single base resolution. B…
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
Hii... i have updated the script in python..But, still getting no data found. Actually the data is there, i have print the parsed html file…
Comment: How to assign cell types after integration in scRNA
by
ATpoint
82k
https://bioconductor.org/books/release/OSCA.multisample/using-corrected-values.html
Comment: Downloading full alignments from Pfam
by
GenoMax
141k
Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
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