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 week
all time
today
this week
this month
this year
180 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
1
vote
4
replies
402
views
some error in building kraken2 database
metagenome
kraken2
updated 3 days ago by
GenoMax
142k • written 4 weeks ago by
Art1ess
• 0
2
votes
4
replies
274
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
3 days ago by
Arton
▴ 10
0
votes
4
replies
221
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
3 days ago by
reza
▴ 300
1
vote
3
replies
910
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 3 days ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
0
votes
3
replies
304
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 4 days ago by
colindaven
6.4k • written 5 days ago by
Bjorn
• 0
1
vote
3
replies
203
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 4 days ago by
GenoMax
142k • written 4 days ago by
s
• 0
5
votes
3
replies
209
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Christopher
▴ 10
2
votes
3
replies
357
views
Trimming tool
Trimming
updated 5 days ago by
Ram
44k • written 8 days ago by
GeneC
• 0
0
votes
3
replies
216
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
2 days ago by
kmat
• 0
1
vote
3
replies
233
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Wilber0x
▴ 50
1
vote
3
replies
241
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 1 day ago by
Bastien Hervé
5.3k • written 2 days ago by
Sara
▴ 30
0
votes
3
replies
306
views
Tool:
Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux
NovaSeq
Illumina
Demultiplexing
Barcode
1 day ago by
Brian Bushnell
20k
1
vote
3
replies
567
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 5 days ago by
Klaus S
▴ 160 • written 6 weeks ago by
Zeng Hao
▴ 40
0
votes
3
replies
219
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 6 days ago by
Ram
44k • written 6 days ago by
Bioinformatics_begginner
▴ 20
0
votes
3
replies
327
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 2 days ago by
ATpoint
82k • written 2 days ago by
shahzaibali
• 0
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 3 days ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
1
vote
3
replies
297
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 2 days ago by
Jeremy
▴ 910 • written 3 days ago by
Mohamed Samir
▴ 30
0
votes
3
replies
180
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 4 days ago by
Ram
44k • written 5 days ago by
pirku
• 0
0
votes
3
replies
266
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 5 days ago by
marco.barr
▴ 130 • written 6 days ago by
Mohamed Samir
▴ 30
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 4 days ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
3
votes
3
replies
226
views
Unexpected read length from NGS
NGS
Illumina
2 days ago by
QX
• 0
0
votes
3
replies
193
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 4 days ago by
GenoMax
142k • written 4 days ago by
bioinfo
▴ 150
1
vote
3
replies
207
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 4 days ago by
Pierre Lindenbaum
162k • written 5 days ago by
mrk
• 0
1
vote
3
replies
259
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 6 days ago by
GenoMax
142k • written 7 days ago by
KHURRAM SHAHZAD
• 0
1
vote
3
replies
310
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
4 days ago by
Pegasus
▴ 100
2
votes
3
replies
230
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
2 days ago by
hashim.rana11
▴ 20
0
votes
3
replies
251
views
z-score of gene set
z-score
scRNA
gene-set
4 days ago by
Hien
• 0
4
votes
2
replies
174
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
indexing
salmon
updated 1 day ago by
Rob
6.6k • written 1 day ago by
Tonya S.
▴ 10
1
vote
2
replies
303
views
Error when i use EVidenceModeler to do the genome annotation
EVidenceModeler
annotation
genome
1 day ago by
peanut
• 0
0
votes
2
replies
213
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
4 days ago by
Shukai
• 0
1
vote
2
replies
192
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 4 days ago by
Ram
44k • written 5 days ago by
Harshita
• 0
1
vote
2
replies
393
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 4 days ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
2
replies
288
views
How can I calculate the OS of each patient?
overall-survival
5 days ago by
Pedro
• 0
1
vote
2
replies
248
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
2 days ago by
F110152169
• 0
0
votes
2
replies
416
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
4 days ago by
ezz3
• 0
0
votes
2
replies
217
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
5 days ago by
sainavyav22
• 0
0
votes
2
replies
194
views
vcf phasing
beagle
WhatsHap
phasing
4 days ago by
safeassli
▴ 10
1
vote
2
replies
200
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 6 days ago by
Ram
44k • written 6 days ago by
Sony
▴ 10
0
votes
2
replies
670
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 3 days ago by
June
• 0 • written 10 months ago by
rkb965
• 0
1
vote
2
replies
363
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 6 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
3
votes
2
replies
215
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 4 days ago by
GenoMax
142k • written 5 days ago by
ashkan
▴ 160
3
votes
2
replies
187
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
3 days ago by
Tuấn Anh
• 0
3
votes
2
replies
176
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 3 days ago by
ATpoint
82k • written 3 days ago by
egascon
• 0
1
vote
2
replies
239
views
Construction of circos plot from WGS data
WGS
Circos
2 days ago by
Anitha
▴ 10
0
votes
2
replies
183
views
CreateSeuratObject taking very long
seurat
2 days ago by
eae6d2e7
• 0
0
votes
2
replies
226
views
What do the transcript variant # mean in RefSeq?
refseq
updated 2 days ago by
Ram
44k • written 3 days ago by
curious
▴ 750
0
votes
2
replies
235
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Varsha
• 0
1
vote
2
replies
217
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
5 days ago by
ojaswinipandey
• 0
1
vote
2
replies
244
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 5 days ago by
colindaven
6.4k • written 6 days ago by
Dr.
• 0
0
votes
1
reply
141
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 2 days ago by
cmdcolin
★ 3.8k • written 3 days ago by
adarsh_pp
▴ 40
180 results • Page
2 of 4
Recent Votes
Answer: How to scrape BioMart data from https://sorfs.ugent.be/ website
Low DESeq2 Sensivity on scRNA Pseudobulk Samples
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
Problem with Ensembl version identifiers after running DESeq2
Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
Recent Locations •
All
United States,
2 minutes ago
Taiwan,
3 minutes ago
France,
5 minutes ago
Turkey,
10 minutes ago
Germany,
10 minutes ago
Cambridge, MA,
11 minutes ago
United States,
14 minutes ago
Recent Awards •
All
Scholar
to
colindaven
6.4k
Popular Question
to
Maria
• 0
Popular Question
to
rj.rezwan
• 0
Popular Question
to
wonde2000
• 0
Teacher
to
alanh
▴ 170
Popular Question
to
Pegasus
▴ 100
Teacher
to
Rob
6.6k
Recent Replies
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
44k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
Alexandra
• 0
Thank you for your response! Interesting paper.
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
Pierre Lindenbaum
162k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
@jaredandrews07 If I integrate using Donor: ```R RunHarmony(seu_obj, group.by.vars = c("Donor_ID")) ``` Should I also normalize my data…
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
QX
• 0
thank you so much!
Answer: Attempt to set 'rownames' on an object with no dimensions
by
elbakri.fatimazahrae
• 0
hello everyone, I got the same error for a function immuCellAI_new; result <- ImmuCellAI_new(countData = expr_data_log22, data_type = "rnas…
Comment: Merging multiple samples in Seurat
by
Picasa
▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
ATpoint
82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation
by
peanut
• 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon
by
Tonya S.
▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon
by
Rob
6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
GenoMax
142k
> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Traffic: 1407 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