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
319 results • Page
2 of 7
Sort: replies
Rank
Views
Votes
Replies
0
votes
4
replies
309
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
3
votes
4
replies
330
views
Truncated metadata file report from ENA Portal API
ena
python
8 days ago by
Giulia
• 0
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 26 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
0
votes
3
replies
263
views
Software to separate reads from different individuals
software
development
nanopore
updated 19 days ago by
GenoMax
142k • written 19 days ago by
njornet
▴ 20
0
votes
3
replies
353
views
Snakemake wrapper issue
fastqc
snakemake
updated 5 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
209
views
How to access GWAVA software of data
GWAVA
updated 5 days ago by
GenoMax
142k • written 5 days ago by
nonaddldy
▴ 10
1
vote
3
replies
293
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 8 days ago by
Ram
43k • written 8 days ago by
Omics data mining
▴ 260
1
vote
3
replies
340
views
some error in building kraken2 database
metagenome
kraken2
25 days ago by
Art1ess
• 0
0
votes
3
replies
324
views
KEGG Pathways
r
RNA-seq
updated 18 days ago by
Ram
43k • written 19 days ago by
Sudip
• 0
2
votes
3
replies
352
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 9 days ago by
bk11
★ 2.5k • written 14 days ago by
Yoosef
▴ 60
1
vote
3
replies
343
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
13 days ago by
Lada
▴ 30
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
1
vote
3
replies
298
views
Odd alignment question/finding
Alignment
updated 16 days ago by
barslmn
★ 2.2k • written 17 days ago by
poordumbsillyidiot
• 0
0
votes
3
replies
170
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
4 days ago by
Esraa
• 0
1
vote
3
replies
330
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 18 days ago by
GenoMax
142k • written 18 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
384
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 20 days ago by
ATpoint
82k • written 21 days ago by
Francesco
▴ 10
1
vote
3
replies
265
views
STAR aligner error
RNA-seq
STAR
slurm
updated 10 days ago by
Ram
43k • written 11 days ago by
M.
▴ 30
0
votes
3
replies
368
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 19 days ago by
Ram
43k • written 5 months ago by
Fadi
• 0
1
vote
3
replies
309
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
26 days ago by
WouterDeCoster
47k
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
0
votes
3
replies
279
views
Sam file Header problem
Sam
Header
problem
file
updated 2 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
saifulislam99121
• 0
0
votes
3
replies
197
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 11 days ago by
GenoMax
142k • written 12 days ago by
Assa Yeroslaviz
★ 1.8k
2
votes
3
replies
333
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 15 days ago by
dthorbur
★ 2.0k • written 16 days ago by
Vijith
▴ 30
0
votes
3
replies
324
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 19 days ago by
GenoMax
142k • written 19 days ago by
kim
• 0
1
vote
3
replies
454
views
PCA plot
DESeq2
PCAplot
updated 20 days ago by
LauferVA
4.2k • written 24 days ago by
Aaliya
▴ 10
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 15 days ago by
Ruqaiya
• 0 • written 10.3 years ago by
Yuelin
▴ 20
0
votes
2
replies
289
views
Downloading older version of a tool
Alignment
tools
15 days ago by
Ruqaiya
• 0
0
votes
2
replies
219
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 10 days ago by
Adam
▴ 30 • written 11 days ago by
Darya
• 0
0
votes
2
replies
186
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
5 days ago by
IdaHao0921
• 0
2
votes
2
replies
249
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
txema.heredia
▴ 130
1
vote
2
replies
284
views
alignment result
RNA-seq
samtools
hisat2
24 days ago by
ahmad.sajad4541
• 0
0
votes
2
replies
236
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 10 days ago by
swbarnes2
14k • written 12 days ago by
ahmad.sajad4541
• 0
1
vote
2
replies
231
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
2 days ago by
bioinfo
▴ 150
0
votes
2
replies
212
views
Output file of samtools flagstat empty
samtools-flagstat
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
ramendra.sarma
• 0
0
votes
2
replies
192
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
4 days ago by
melissa.joubert
• 0
3
votes
2
replies
198
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
0
votes
2
replies
297
views
Traveler with Infernal mapping failed
r2dt
updated 15 hours ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
0
votes
2
replies
202
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
20 days ago by
Lluís R.
★ 1.2k
0
votes
2
replies
275
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
11 days ago by
sainavyav22
• 0
0
votes
2
replies
370
views
How to update R on ubuntu
installation
update
R
apt-get
19 days ago by
Bosberg
▴ 50
0
votes
2
replies
218
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
1
vote
2
replies
325
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
18 days ago by
Nafi
• 0
0
votes
2
replies
315
views
Annovar using R package
Annovar
gnomAD
R
23 days ago by
DKA
▴ 40
0
votes
2
replies
235
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
6 days ago by
analyst
▴ 50
0
votes
2
replies
310
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
yahn
• 0
1
vote
2
replies
294
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
17 days ago by
rianna.collins
• 0
0
votes
2
replies
221
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
10 days ago by
Nicholas
• 0
1
vote
2
replies
257
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 18 days ago by
Ram
43k • written 19 days ago by
Ravita
• 0
0
votes
2
replies
249
views
What should I consider as FASTA for dataset?
PDB
FASTA
19 days ago by
Nafi
• 0
0
votes
2
replies
324
views
bam merging for archaic samples
samtools
bam
updated 27 days ago by
Ram
43k • written 29 days ago by
Matteo Ungaro
▴ 100
319 results • Page
2 of 7
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
Turkey,
6 minutes ago
Irbid,
7 minutes ago
United States,
21 minutes ago
United Kingdom,
23 minutes ago
Italy,
24 minutes ago
UK,
24 minutes ago
United States,
27 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
Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
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 -…
Traffic: 1354 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