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484 results • Page
3 of 10
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0
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3
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624
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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
212
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 8 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
321
views
PCA plot
DESeq2
PCAplot
updated 7 hours ago by
LauferVA
4.2k • written 3 days ago by
Aaliya
▴ 10
1
vote
3
replies
230
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
5 days ago by
WouterDeCoster
47k
3
votes
3
replies
480
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 8 days ago by
swbarnes2
14k • written 9 days ago by
noodle
▴ 530
0
votes
3
replies
286
views
How do I handle it if there are multiple ENSEMBL IDs in one gene symbol in the scRNA sequencing data?
Seurat
scRNA-seq
count-matrix
20 days ago by
Jeyong
• 0
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
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
0
votes
3
replies
275
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
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
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
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
271
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
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 12 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
0
votes
3
replies
268
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 19 days ago by
noodle
▴ 530 • written 19 days ago by
CrisRisu
• 0
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 6 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
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
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
259
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
0
votes
2
replies
275
views
How to get genes in a gene set in msigdb?
msigdb
23 days ago by
Chris
▴ 260
0
votes
2
replies
375
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
28 days ago by
Samuel
▴ 20
1
vote
2
replies
280
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
2
votes
2
replies
631
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 12 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
1
vote
2
replies
275
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
12 days ago by
bioinfo
▴ 150
0
votes
2
replies
273
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
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
811
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 12 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
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
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy
SPAdes
updated 26 days ago by
Ram
43k • written 2.4 years ago by
adnan.lahuf
• 0
0
votes
2
replies
542
views
autodockvina
python
python3
autodock
updated 10 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
0
votes
2
replies
271
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
241
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
82
views
PDB related issue
rcsb
pdb
updated 2 hours ago by
noodle
▴ 530 • written 5 hours ago by
Nafi
• 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
0
votes
2
replies
252
views
Problem with downloading genome in SnpEff
SnpEff
18 days ago by
Javier
• 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
0
votes
2
replies
262
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 12 days ago by
Ram
43k • written 13 days ago by
David
• 0
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
255
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
11 days ago by
DKA
▴ 40
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
0
votes
2
replies
381
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
9 days ago by
Ashok
• 0
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
1
vote
2
replies
222
views
alignment result
RNA-seq
samtools
hisat2
3 days ago by
ahmad.sajad4541
• 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
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
0
votes
2
replies
543
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
10 days ago by
航太郎
• 0
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 23 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
484 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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Recent Replies
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
Gordon Smyth
★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
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…
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