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484 results • Page
3 of 10
Sort: replies
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Views
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Replies
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta
Nanopore
long-read
fastq
updated 23 days ago by
Ram
43k • written 2.9 years ago by
K
▴ 10
2
votes
3
replies
931
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 13 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 10 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
1
vote
3
replies
1.8k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 23 days ago by
Ram
43k • written 2.3 years ago by
matt81rd
▴ 10
0
votes
3
replies
624
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 26 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
1
vote
3
replies
201
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 4 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 10 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
1
vote
3
replies
360
views
Ensembl gene id conversion
biomart
ensembl
updated 12 days ago by
ATpoint
82k • written 14 days ago by
naveedhasan2000
• 0
3
votes
3
replies
335
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
29 days ago by
Pumla
• 0
0
votes
3
replies
325
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 15 days ago by
ATpoint
82k • written 17 days ago by
gdfsnkfns
• 0
1
vote
3
replies
355
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 27 days ago by
Pierre Lindenbaum
161k • written 28 days ago by
Max
• 0
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq
deseq2
Differential-Gene-expression
R
updated 19 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 11 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
0
votes
3
replies
267
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 19 days ago by
noodle
▴ 530 • written 19 days ago by
CrisRisu
• 0
0
votes
3
replies
270
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 17 days ago by
GenoMax
141k • written 17 days ago by
neish
• 0
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 13 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
0
votes
3
replies
262
views
can't download and use mageck-vispr for R?
mageck-vispr
Rstudio
updated 26 days ago by
ATpoint
82k • written 27 days ago by
Vishal
• 0
1
vote
3
replies
395
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 20 days ago by
Ram
43k • written 23 days ago by
catherinemaria2728
• 0
2
votes
3
replies
258
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics
RNA-Seq
p-value
updated 26 days ago by
Ram
43k • written 26 days ago by
Netanel
• 0
1
vote
3
replies
229
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
5 days ago by
WouterDeCoster
47k
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 10 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
0
votes
3
replies
274
views
Highest variable features in single cell data
single-cell
updated 2 days ago by
bk11
★ 2.4k • written 3 days ago by
Kazo
• 0
0
votes
2
replies
272
views
bam merging for archaic samples
samtools
bam
updated 7 days ago by
Ram
43k • written 8 days ago by
Matteo Ungaro
▴ 100
0
votes
2
replies
251
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 4 days ago by
Ram
43k • written 5 days ago by
v.berriosfarias
▴ 140
4
votes
2
replies
234
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 24 days ago by
Pierre Lindenbaum
161k • written 24 days ago by
Lee
• 0
1
vote
2
replies
240
views
permutation test in edgeR
rna-seq
edgeR
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 20 days ago by
Netanel
• 0
0
votes
2
replies
322
views
GSEA analysis in R
GSEA
R
Arabidopsis
10 days ago by
Sudip
• 0
0
votes
2
replies
252
views
Problem with downloading genome in SnpEff
SnpEff
18 days ago by
Javier
• 0
0
votes
2
replies
625
views
Seeking Alternative Tools for Predicting Mature microRNAs from Vertebrate Animal Precursors in In Silico Study
mirdeep2
maturebayes
microrna
updated 26 days ago by
Ram
43k • written 12 months ago by
Beatriz
• 0
2
votes
2
replies
276
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 17 days ago by
ATpoint
82k • written 17 days ago by
Shicheng Guo
★ 9.4k
1
vote
2
replies
321
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 13 days ago by
Istvan Albert
100k • written 14 days ago by
Jiang
• 0
0
votes
2
replies
229
views
Bedmethyl file format
bedmethyl
methylation
updated 11 days ago by
GenoMax
141k • written 11 days ago by
njornet
▴ 20
2
votes
2
replies
631
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 11 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
0
votes
2
replies
381
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
9 days ago by
Ashok
• 0
0
votes
2
replies
226
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
16 days ago by
marongiu.luigi
▴ 710
1
vote
2
replies
221
views
alignment result
RNA-seq
samtools
hisat2
3 days ago by
ahmad.sajad4541
• 0
0
votes
2
replies
270
views
Regions not clear in VCF
whole-exome
variant-calling
updated 20 days ago by
Ram
43k • written 21 days ago by
priya.bmg
▴ 60
1
vote
2
replies
279
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 11 days ago by
Ram
43k • written 11 days ago by
aniigodwinn
• 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 10 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
2
replies
513
views
Gene expression assay Yeast sample prep
Live-cells
updated 26 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
1
vote
2
replies
209
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
20 days ago by
phhelou5
• 0
0
votes
2
replies
418
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
9 days ago by
Ashok
• 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 11 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
0
votes
2
replies
255
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
11 days ago by
mropri
▴ 150
0
votes
2
replies
297
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
12 days ago by
Koketso
• 0
1
vote
2
replies
927
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 23 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
0
votes
2
replies
242
views
Annovar using R package
Annovar
gnomAD
R
3 days ago by
DKA
▴ 40
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 12 days ago by
Ram
43k • written 3.0 years ago by
Mat
▴ 60
0
votes
2
replies
268
views
WGCNA
PCA
WGCNA
EIGENGENE
16 days ago by
rajasekargutha
▴ 60
0
votes
2
replies
542
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
9 days ago by
航太郎
• 0
484 results • Page
3 of 10
Recent Votes
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
Answer: How to use limma to find differentially expressed genes in response to a continu
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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) …
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by
chujie
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Hi, I met the same problem, have you found the solution?
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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 …
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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…
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Jeremy Leipzig
22k
i have the name ready: out**liar**
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141k
Sequencing by hybridization (https://en.wikipedia.org/wiki/Sequencing_by_hybridization ) is likely not giving you single base resolution. B…
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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…
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https://bioconductor.org/books/release/OSCA.multisample/using-corrected-values.html
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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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by
GenoMax
141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
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