Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
484 results • Page
4 of 10
Sort: replies
Rank
Views
Votes
Replies
1
vote
2
replies
928
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
1
vote
2
replies
248
views
What are crucial apps/ scripts for cancer genome/data analysis that can be set up as an web based app?
web
based
cancer
updated 26 days ago by
LauferVA
4.2k • written 27 days ago by
bartek
• 0
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
825
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 26 days ago by
Ram
43k • written 2.7 years ago by
Mohan
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 10 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 270
0
votes
2
replies
428
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
9 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
418
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
9 days ago by
Ashok
• 0
0
votes
2
replies
322
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
15 days ago by
O.rka
▴ 710
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 11 days ago by
Ram
43k • written 4.4 years ago by
akutasame
▴ 40
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
322
views
GSEA analysis in R
GSEA
R
Arabidopsis
10 days ago by
Sudip
• 0
0
votes
2
replies
243
views
Annovar using R package
Annovar
gnomAD
R
3 days ago by
DKA
▴ 40
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
542
views
autodockvina
python
python3
autodock
updated 10 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
2
votes
2
replies
266
views
Removing adapters in all the RNAseq samples regardless if they have or not, is it correct?
fastqc
trimming
adapters
cutadapt
RNAseq
updated 25 days ago by
dsull
★ 5.9k • written 25 days ago by
ev97
▴ 20
0
votes
2
replies
873
views
freebayes calls presumably homozygous variants as heterozygotes
SNP
freebayes
variant-call
genotyping
updated 23 days ago by
virginia.baraja
• 0 • written 3.1 years ago by
johanna.pieplow
• 0
0
votes
2
replies
316
views
Adding Clinvar data source to funcotator
gatk
Clinvar
funcotator
gnomad
updated 28 days ago by
Pierre Lindenbaum
161k • written 28 days ago by
Mojtaba
• 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
3
votes
2
replies
305
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics
Single-Cell
updated 23 days ago by
Ram
43k • written 8 weeks ago by
Daddy
▴ 20
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
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
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
1
vote
2
replies
226
views
convert a seurat object to expressionset
Seurat
17 days ago by
Bine
▴ 60
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
0
votes
2
replies
268
views
WGCNA
PCA
WGCNA
EIGENGENE
16 days ago by
rajasekargutha
▴ 60
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
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
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
221
views
RNA-Seq isoforms identification
RNA-seq
updated 25 days ago by
Andres
▴ 20 • written 25 days ago by
latita.atun
• 0
1
vote
2
replies
335
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 25 days ago by
jkbonfield
★ 1.2k • written 6 weeks ago by
geocarvalho
▴ 360
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
275
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
16 days ago by
ramin.k2013
• 0
0
votes
2
replies
270
views
RNAseq 1 control 2 different treatment
RNA-seq
12 days ago by
matteo.levorato
• 0
0
votes
2
replies
202
views
Can't figure out plink --sample-diff
plink
18 days ago by
curious
▴ 750
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
579
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 23 days ago by
Ram
43k • written 22 months ago by
priya.bmg
▴ 60
0
votes
2
replies
255
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
11 days ago by
DKA
▴ 40
1
vote
1
reply
227
views
Retrieve a % coverage for each transcript
RNA-seq
updated 11 days ago by
Ram
43k • written 11 days ago by
jammydodger123456
▴ 40
0
votes
1
reply
213
views
merging Seurat objects after SCT
Seurat
SCT
updated 13 days ago by
Ram
43k • written 13 days ago by
michelle.swarovski
• 0
0
votes
1
reply
188
views
samflags to removes mapped concordantly >1 times
samtools
Bowtie2
Metagenome
updated 17 days ago by
jkbonfield
★ 1.2k • written 24 days ago by
pompam_5904
• 0
0
votes
1
reply
235
views
Data table for LOEUF loss-of-function observed/expected upper bound fraction
LOEUF
updated 24 days ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
Shicheng Guo
★ 9.4k
0
votes
1
reply
191
views
Freyja plot error
Freyja
updated 11 days ago by
Ram
43k • written 11 days ago by
Adyasha
• 0
1
vote
1
reply
183
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 12 days ago by
dsull
★ 5.9k • written 12 days ago by
niruf
• 0
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 11 days ago by
Ram
43k • written 6.8 years ago by
Dipro
• 0
0
votes
1
reply
186
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 18 days ago by
Pierre Lindenbaum
161k • written 18 days ago by
Saran
▴ 50
0
votes
1
reply
161
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 5 days ago by
bk11
★ 2.4k • written 5 days ago by
alphaflylizard
• 0
0
votes
1
reply
456
views
principal coordinate analysis
PCoA
R
updated 26 days ago by
Ram
43k • written 10 months ago by
rene.j.erhardt
▴ 20
2
votes
1
reply
284
views
Forgot the web site with comparison of NGS platforms
NGS
platforms
updated 29 days ago by
cmdcolin
★ 3.8k • written 29 days ago by
konstantinkul
▴ 110
0
votes
1
reply
229
views
How do I know whether it is not a failure of ChIPseq data
ChIPseq
updated 21 days ago by
dthorbur
★ 1.9k • written 23 days ago by
Herman Einstein
• 0
484 results • Page
4 of 10
Recent Votes
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
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
Recent Locations •
All
Mexico,
just now
Hong Kong,
3 minutes ago
United States,
8 minutes ago
Whitefish, MT,
9 minutes ago
United States,
11 minutes ago
United States,
11 minutes ago
South Korea,
15 minutes ago
Recent Awards •
All
Teacher
to
Jeremy Leipzig
22k
Popular Question
to
AshleeThomson
▴ 80
Popular Question
to
michael.flower.14
▴ 180
Popular Question
to
Nitin Narwade
★ 1.6k
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
rj.rezwan
• 0
Popular Question
to
husensofteng
▴ 410
Recent Replies
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
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
▴ 540
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 …
Traffic: 1872 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6