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
682 results • Page
2 of 14
Sort: Votes
Rank
Views
Votes
Replies
4
votes
1
reply
360
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
19 days ago by
pairedttest
▴ 10
4
votes
1
reply
269
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 13 days ago by
zx8754
11k • written 14 days ago by
Jautis
▴ 560
4
votes
1
reply
207
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
4 days ago by
J.
▴ 40
4
votes
2
replies
271
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 14 days ago by
Ram
43k • written 16 days ago by
carolofharvest
▴ 40
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 10 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
4
votes
7
replies
493
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 1 day ago by
marco.barr
▴ 130 • written 3 days ago by
diqixiaoyaoer
▴ 20
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 9 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 12 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
8
replies
774
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 22 days ago by
Alex Reynolds
35k • written 23 days ago by
J
▴ 10
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 19 days ago by
Andres
▴ 20 • written 9.7 years ago by
hermathena
▴ 40
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 11 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 5 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
4
votes
11
replies
898
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 25 days ago by
LauferVA
4.2k • written 26 days ago by
dominickd
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
19 days ago by
anna
▴ 20
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 10 days ago by
Pierre Lindenbaum
161k • written 10 days ago by
Lila M
★ 1.2k
4
votes
7
replies
431
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
5 days ago by
Chen
• 0
4
votes
2
replies
276
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
10 days ago by
mnx0723
• 0
4
votes
7
replies
616
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 24 days ago by
dsull
★ 6.0k • written 25 days ago by
VITALA
• 0
4
votes
9
replies
455
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
1 day ago by
Gabriel R.
★ 2.9k
4
votes
6
replies
811
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 22 days ago by
dsull
★ 6.0k • written 26 days ago by
qudrat.nii
▴ 10
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 15 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 15 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
4
votes
7
replies
639
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
19 days ago by
e.r.zakiev
▴ 210
3
votes
5
replies
358
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 27 days ago by
GenoMax
142k • written 27 days ago by
ahmad.sajad4541
• 0
3
votes
8
replies
712
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 12 days ago by
Chris Dean
▴ 410 • written 16 days ago by
sovrappensiero
▴ 100
3
votes
5
replies
647
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
27 days ago by
n_navy
• 0
3
votes
1
reply
209
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 9 days ago by
dthorbur
★ 2.0k • written 9 days ago by
Eren
• 0
3
votes
1
reply
286
views
Seurat merge and batch correction
Seurat
updated 25 days ago by
Ram
43k • written 26 days ago by
sooni
▴ 20
3
votes
3
replies
557
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 29 days ago by
swbarnes2
14k • written 4 weeks ago by
noodle
▴ 580
3
votes
2
replies
196
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 6 days ago by
ATpoint
82k • written 6 days ago by
jennyp0706
• 0
3
votes
3
replies
374
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 23 days ago by
GenoMax
142k • written 23 days ago by
sapuizait
▴ 10
3
votes
3
replies
371
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 23 days ago by
swbarnes2
14k • written 23 days ago by
M
• 0
3
votes
3
replies
384
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 16 days ago by
ATpoint
82k • written 17 days ago by
alifafiq1
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
3
replies
297
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 26 days ago by
GenoMax
142k • written 27 days ago by
Mariana
▴ 40
3
votes
4
replies
316
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 1 day ago by
Jeremy Leipzig
22k • written 3 days ago by
Ali
• 0
3
votes
3
replies
274
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 26 days ago by
Mensur Dlakic
★ 27k • written 26 days ago by
c_u
▴ 520
3
votes
0
replies
157
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 25 days ago by
Ram
43k • written 25 days ago by
carlopecoraro2
★ 2.5k
3
votes
4
replies
424
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
23 days ago by
QX
• 0
3
votes
6
replies
762
views
Ciriquant not configuring hisat2 indexed files
ciriquant
27 days ago by
Atul K.
• 0
3
votes
3
replies
291
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 5 days ago by
Ram
43k • written 19 days ago by
Adyasha
• 0
3
votes
4
replies
761
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
26 days ago by
rahu
• 0
3
votes
1
reply
218
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 6 days ago by
aw7
▴ 300 • written 10 days ago by
Zeng Hao
▴ 40
3
votes
3
replies
287
views
what is another word for a BLAST "hit"?
blast
alignment
8 days ago by
dec986
▴ 380
3
votes
5
replies
411
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
15 days ago by
Maverick
▴ 10
3
votes
5
replies
350
views
Generating mpileup file using samtools
mpileup
samtools
updated 16 days ago by
Joe
21k • written 16 days ago by
Ruqaiya
• 0
3
votes
2
replies
321
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
26 days ago by
kristiewyleung
• 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 16 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
14 days ago by
Ibrahim Tanyalcin
★ 1.2k
682 results • Page
2 of 14
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Recent Locations •
All
United States,
1 minute ago
Italy,
1 minute ago
Norway,
3 minutes ago
Pakistan,
7 minutes ago
Saudi Arabia,
7 minutes ago
Italy,
7 minutes ago
United States,
7 minutes ago
Recent Awards •
All
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
to
Muhammad
• 0
Popular Question
to
synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
Popular Question
to
syedahamdani94
• 0
Popular Question
to
mohammadhassanj
▴ 260
Recent Replies
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Traffic: 1406 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