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321 results • Page
2 of 7
Sort: Views
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Views
Votes
Replies
0
votes
4
replies
423
views
Highest variable features in single cell data
single-cell
11 days ago by
carolofharvest
▴ 40
3
votes
7
replies
421
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
19 days ago by
salias
• 0
1
vote
4
replies
417
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 8 days ago by
GenoMax
142k • written 4 weeks ago by
aniigodwinn
• 0
1
vote
6
replies
412
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 15 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by
beginner123
• 0
1
vote
9
replies
405
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 8 days ago by
i.sudbery
19k • written 11 days ago by
Assa Yeroslaviz
★ 1.8k
2
votes
4
replies
384
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
24 days ago by
samuelkalandarov2002
▴ 10
1
vote
3
replies
380
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
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
3
replies
367
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
2
replies
363
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 5 days ago by
Ram
43k • written 6 days ago by
t.fortunato.asquini
• 0
0
votes
3
replies
349
views
Snakemake wrapper issue
fastqc
snakemake
updated 4 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
1
vote
4
replies
347
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 3 days ago by
Juke34
8.6k • written 5 days ago by
Vijith
▴ 30
3
votes
5
replies
346
views
Generating mpileup file using samtools
mpileup
samtools
updated 15 days ago by
Joe
21k • written 15 days ago by
Ruqaiya
• 0
2
votes
3
replies
342
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 9 days ago by
bk11
★ 2.5k • written 13 days ago by
Yoosef
▴ 60
1
vote
3
replies
342
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
13 days ago by
Lada
▴ 30
1
vote
3
replies
340
views
some error in building kraken2 database
metagenome
kraken2
24 days ago by
Art1ess
• 0
2
votes
2
replies
337
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 24 days ago by
Ram
43k • written 25 days ago by
v.berriosfarias
▴ 140
0
votes
0
replies
336
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
15 days ago by
NorbertK
▴ 10
2
votes
3
replies
331
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 15 days ago by
Vijith
▴ 30
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
0
votes
0
replies
330
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
24 days ago by
pramach1
▴ 40
0
votes
1
reply
325
views
Could you please assist in identifying this cluster?
single-cell
updated 29 days ago by
Ram
43k • written 29 days ago by
carolofharvest
▴ 40
0
votes
3
replies
324
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 18 days ago by
GenoMax
142k • written 19 days ago by
kim
• 0
1
vote
2
replies
324
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
17 days ago by
Nafi
• 0
3
votes
4
replies
324
views
Truncated metadata file report from ENA Portal API
ena
python
8 days ago by
Giulia
• 0
0
votes
2
replies
324
views
bam merging for archaic samples
samtools
bam
updated 27 days ago by
Ram
43k • written 28 days ago by
Matteo Ungaro
▴ 100
0
votes
5
replies
323
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
5 days ago by
SilhouetteQ
• 0
5
votes
5
replies
323
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
10 days ago by
Chris
▴ 280
0
votes
3
replies
323
views
KEGG Pathways
r
RNA-seq
updated 18 days ago by
Ram
43k • written 18 days ago by
Sudip
• 0
0
votes
2
replies
315
views
Annovar using R package
Annovar
gnomAD
R
23 days ago by
DKA
▴ 40
1
vote
5
replies
311
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 1 day ago by
dthorbur
★ 2.0k • written 2 days ago by
BATMAN
• 0
0
votes
4
replies
310
views
Correlation Analysis
statistics
methylation
NGS
expression
7 days ago by
Researcher
▴ 30
0
votes
4
replies
308
views
Genbank File Format
gbkformat
18 days ago by
alenew.am
• 0
1
vote
3
replies
307
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
25 days ago by
WouterDeCoster
47k
0
votes
2
replies
307
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
4
replies
305
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 11 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
0
votes
1
reply
305
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 29 days ago by
GenoMax
142k • written 29 days ago by
bioyas
▴ 10
0
votes
1
reply
301
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 11 days ago by
andres.firrincieli
3.6k • written 12 days ago by
Antonio
• 0
0
votes
2
replies
299
views
How are score_weights calculated in this code?
single-cell
7 days ago by
carolofharvest
▴ 40
1
vote
3
replies
294
views
Odd alignment question/finding
Alignment
updated 15 days ago by
barslmn
★ 2.2k • written 16 days ago by
poordumbsillyidiot
• 0
1
vote
2
replies
294
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
16 days ago by
rianna.collins
• 0
0
votes
4
replies
291
views
Merge clusters in Seurat UMAP
seurat
umap
1 day ago by
kilcdincer
▴ 10
1
vote
3
replies
291
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
0
votes
2
replies
288
views
Downloading older version of a tool
Alignment
tools
14 days ago by
Ruqaiya
• 0
0
votes
5
replies
286
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
chrisk
• 0
0
votes
6
replies
285
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
1 day ago by
hannes.bongartz
• 0
1
vote
2
replies
285
views
Downloading full alignments from Pfam
pfam
13 days ago by
bef1
• 0
0
votes
5
replies
285
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 10 days ago by
Joe
21k • written 10 days ago by
Lemonhope
• 0
1
vote
2
replies
284
views
alignment result
RNA-seq
samtools
hisat2
23 days ago by
ahmad.sajad4541
• 0
321 results • Page
2 of 7
Recent Votes
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?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
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Recent Replies
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.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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