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185 results • Page
1 of 4
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0
votes
0
replies
6
views
PDB related issue
rcsb
pdb
7 minutes ago by
Nafi
• 0
0
votes
0
replies
13
views
News:
Online course: Genome Annotation
GenomeAssembly
GenomeAnnoration
1 hour ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
80
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 55 minutes ago by
dsull
★ 5.9k • written 2 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 1 hour ago by
chujie
• 0 • written 8 months ago by
Gio
• 0
2
votes
5
replies
335
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
2 hours ago by
ashaneev07
▴ 20
0
votes
1
reply
78
views
Downloading full alignments from Pfam
pfam
updated 4 hours ago by
GenoMax
141k • written 9 hours ago by
bef1
• 0
0
votes
1
reply
683
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 9 hours ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
1
vote
1
reply
172
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 12 hours 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 12 hours ago by
Ram
43k • written 8 months ago by
Calum
▴ 10
0
votes
0
replies
54
views
adjusting for confounders in LMER in R
confounders
LMER
R
13 hours ago by
rene.j.erhardt
▴ 20
0
votes
10
replies
278
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
updated just now by
Mensur Dlakic
★ 27k • written 17 hours ago by
Ruqaiya
• 0
1
vote
3
replies
190
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 2 hours ago by
ATpoint
82k • written 23 hours ago by
Francesco
▴ 10
0
votes
0
replies
83
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
23 hours ago by
tnminh89
▴ 10
9
votes
9
replies
674
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 hour ago by
Jeremy Leipzig
22k • written 1 day ago by
noodle
▴ 530
0
votes
0
replies
89
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
86
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
1
reply
272
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
284
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
269
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
303
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 10 minutes ago by
Mensur Dlakic
★ 27k • written 1 day ago by
O.rka
▴ 710
0
votes
1
reply
176
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
207
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
166
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
pairedttest
▴ 10
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
0
votes
0
replies
400
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
1 day ago by
biocellbio
• 0
4
votes
8
replies
545
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
606
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
274
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
162
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 2 days ago by
Claire Watson
▴ 60
0
votes
2
replies
235
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 1 day ago by
Ram
43k • written 2 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
167
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
2 days ago by
HarperReed
• 0
3
votes
3
replies
240
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
128
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
140
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 1 day ago by
Ram
43k • written 2 days ago by
SineWave
• 0
0
votes
0
replies
135
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
392
views
gvcf joint calling
WES
GATK
VCF
gVCF
11 hours ago by
zihanss
• 0
0
votes
0
replies
127
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
2 days ago by
turcoa1
• 0
3
votes
3
replies
260
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
M
• 0
0
votes
0
replies
138
views
Designing single-stable RNA molecules
structure
RNA
2 days ago by
Edna
• 0
0
votes
0
replies
153
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
2 days ago by
simplitia
▴ 130
0
votes
1
reply
189
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
252
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
285
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 2 days ago by
Ram
43k • written 3 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
285
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
23 hours ago by
Francesco
▴ 10
1
vote
6
replies
390
views
ScRNA data question
scRNA
Vlnplot
Samples
1 day ago by
starswillfade
▴ 10
0
votes
0
replies
152
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
145
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
145
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
3 days ago by
Emily
▴ 10
1
vote
0
replies
160
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
3 days ago by
rohitsatyam102
▴ 850
185 results • Page
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Comment: NGS forensics: how to know if data is fabricated
Answer: How to use limma to find differentially expressed genes in response to a continu
Batch effects : ComBat or removebatcheffects (limma package) ?
How to input margin to UpsetR figure
Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
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Recent Replies
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) …
Answer: 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…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
You can use the default `adapters.fa` file included in the `resources` folder of [**BBMap suite**][1] (program to use is `bbduk.sh`) or a p…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
Only way to find out is to try. It may work but if it is not going to then you will find that out quick (process would likely crash because…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
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