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177 results • Page
2 of 4
Sort: replies
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Views
Votes
Replies
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
19 hours ago by
Aspire
▴ 330
5
votes
4
replies
5.1k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 22 hours ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
0
votes
4
replies
232
views
Where to find old version of GATK best practice
gatk
2 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
4
replies
315
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 2 days ago by
Ram
44k • written 9 days ago by
Arton
▴ 10
1
vote
4
replies
275
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
2 days ago by
shpak.max
▴ 50
0
votes
4
replies
226
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
2 days ago by
shpak.max
▴ 50
0
votes
4
replies
327
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
2 days ago by
Luqman
• 0
5
votes
3
replies
191
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Christopher
▴ 10
1
vote
3
replies
219
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 10 hours ago by
Jeremy
▴ 910 • written 1 day ago by
Mohamed Samir
▴ 30
0
votes
3
replies
162
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 2 days ago by
Ram
44k • written 2 days ago by
pirku
• 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 2 days ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
295
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
2 days ago by
Pegasus
▴ 100
0
votes
3
replies
181
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 2 days ago by
GenoMax
142k • written 2 days ago by
bioinfo
▴ 150
1
vote
3
replies
195
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 2 days ago by
Pierre Lindenbaum
162k • written 2 days ago by
mrk
• 0
0
votes
3
replies
239
views
z-score of gene set
z-score
scRNA
gene-set
2 days ago by
Hien
• 0
1
vote
3
replies
904
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 1 day ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
0
votes
3
replies
210
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 3 days ago by
Ram
44k • written 3 days ago by
Bioinformatics_begginner
▴ 20
0
votes
3
replies
290
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 1 day ago by
colindaven
6.4k • written 3 days ago by
Bjorn
• 0
1
vote
3
replies
558
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 2 days ago by
Klaus S
▴ 160 • written 6 weeks ago by
Zeng Hao
▴ 40
2
votes
3
replies
350
views
Trimming tool
Trimming
updated 3 days ago by
Ram
44k • written 6 days ago by
GeneC
• 0
0
votes
3
replies
256
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 3 days ago by
marco.barr
▴ 130 • written 4 days ago by
Mohamed Samir
▴ 30
1
vote
3
replies
248
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 3 days ago by
GenoMax
142k • written 5 days ago by
KHURRAM SHAHZAD
• 0
1
vote
3
replies
223
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Wilber0x
▴ 50
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 23 hours ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
0
votes
3
replies
195
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 9 hours ago by
ATpoint
82k • written 11 hours ago by
shahzaibali
• 0
1
vote
3
replies
193
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 1 day ago by
GenoMax
142k • written 2 days ago by
s
• 0
0
votes
2
replies
183
views
vcf phasing
beagle
WhatsHap
phasing
2 days ago by
safeassli
▴ 10
0
votes
2
replies
613
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 16 hours ago by
June
• 0 • written 10 months ago by
rkb965
• 0
0
votes
2
replies
272
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 6 days ago by
Pierre Lindenbaum
162k • written 7 days ago by
melissachua90
▴ 70
1
vote
2
replies
194
views
Construction of circos plot from WGS data
WGS
Circos
1 hour ago by
Anitha
▴ 10
1
vote
2
replies
194
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 3 days ago by
Ram
44k • written 4 days ago by
Sony
▴ 10
0
votes
2
replies
211
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
3 days ago by
sainavyav22
• 0
0
votes
2
replies
279
views
How can I calculate the OS of each patient?
overall-survival
3 days ago by
Pedro
• 0
0
votes
2
replies
328
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
2 days ago by
ezz3
• 0
1
vote
2
replies
139
views
Unexpected read length from NGS
NGS
Illumina
updated 19 hours ago by
ATpoint
82k • written 21 hours ago by
QX
• 0
3
votes
2
replies
135
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 19 hours ago by
ATpoint
82k • written 22 hours ago by
egascon
• 0
1
vote
2
replies
212
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
3 days ago by
ojaswinipandey
• 0
0
votes
2
replies
156
views
CreateSeuratObject taking very long
seurat
3 hours ago by
eae6d2e7
• 0
1
vote
2
replies
236
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 2 days ago by
colindaven
6.4k • written 4 days ago by
Dr.
• 0
1
vote
2
replies
358
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 4 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
2
replies
282
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 6 days ago by
LauferVA
4.2k • written 6 days ago by
ijarne
• 0
0
votes
2
replies
152
views
What do the transcript variant # mean in RefSeq?
refseq
updated 12 hours ago by
Ram
44k • written 15 hours ago by
curious
▴ 750
0
votes
2
replies
331
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
4 days ago by
Ezequiel
• 0
1
vote
2
replies
731
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 5 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
0
votes
2
replies
306
views
Traveler with Infernal mapping failed
r2dt
updated 5 days ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
0
votes
2
replies
203
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 21 hours ago by
i.sudbery
19k • written 2 days ago by
Varsha
• 0
3
votes
2
replies
174
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
1 day ago by
Tuấn Anh
• 0
0
votes
2
replies
194
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
2 days ago by
Shukai
• 0
1
vote
2
replies
182
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 2 days ago by
Ram
44k • written 2 days ago by
Harshita
• 0
1
vote
2
replies
386
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 2 days ago by
finch
• 0 • written 3 months ago by
star
▴ 10
177 results • Page
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Answer: Random Access remote BAM files
Answer: How to interpret this plotMDS of three disease clusters?
Comment: How to interpret this plotMDS of three disease clusters?
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
A: Venter Genome Vcf
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
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Comment: Error with BiocParallel. No barcodes files found
by
bio_info
• 0
I understand, thanks for explaining this to me. I'll take care of this in future.
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
by
Pierre Lindenbaum
162k
> , but I was unsuccessful. what does it mean ?
Answer: Does prokka work the same on forward and reverse complementary reads?
by
igmin
• 0
Prokka works the same on both forward and reverse complementary reads. It doesn't matter if your genetic sequences are in their original fo…
Comment: Construction of circos plot from WGS data
by
Anitha
▴ 10
Thank you for the information. But, I am still struggling like which data to use and how to process the input data to represent to build th…
Comment: Tools for chromosomal aneuploidy detection
by
cmdcolin
★ 3.8k
is there any reason why you do not like tools based on read depths?
Comment: CreateSeuratObject taking very long
by
eae6d2e7
• 0
Thank you for your reply! I followed your advice to convert to sparse matrix first but I got this error Error in Matrix::sparseMatrix(raw_…
Answer: Venter Genome Vcf
by
ericrkofman
▴ 20
I can't find an hg38 version, and the old VCF seems to be of a different header format so I am having difficulty converting it to hg38 from…
Comment: What is a good way to do gene differentials in single cell data where one group
by
ATpoint
82k
Preferred if you have true biological replicates. Can still be combined with my subsetting strategy, like use 100x different cells for the …
Answer: ComplexHeatmap - How to change fontsize of rowAnnotation
by
ATpoint
82k
```r set.seed(1) m = matrix(rnorm(100), nrow = 10) rownames(m) = 1:10 # normal ha = rowAnnotation(foo = anno_mark(at=1:nrow(m), labels=row…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
44k
Please do not add answers unless you're actually answering the question. I've moved your post to a comment.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
I still cannot find a way. It seems to be an easy to solve issue and I was trying any possible combination with the aforementioned gp=gpar(…
Comment: What is a good way to do gene differentials in single cell data where one group
by
fracarb8
★ 1.6k
I would probably use a pseudobulk approach.
Comment: Error when looping over multiple columns in a data frame in R
by
Jeremy
▴ 910
`cutpoint_results[[col_name]]` adds each new cut point to the list entitled "cutpoint_results", while keeping the original column names fr…
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
by
swbarnes2
14k
Never use uncorrected p-values with RNASeq. Your PCA is suggesting that your sample groups are not very different, and the DEG tests con…
Comment: What is a good way to do gene differentials in single cell data where one group
by
ATpoint
82k
I would keep it transparent. Do DE by subsetting large to small group. Do that randomly many times, then either average stats or use some s…
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