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347 results • Page
2 of 7
Sort: Views
Rank
Views
Votes
Replies
1
vote
7
replies
540
views
Question regarding WGCNA
WGCNA
Network-construction
8 days ago by
deepak
• 0
2
votes
5
replies
539
views
Marking duplicates using UMIs
Deduplication
UMI
updated 25 days ago by
i.sudbery
19k • written 26 days ago by
Lipika
• 0
0
votes
1
reply
537
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 22 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
1
vote
1
reply
524
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
28 days ago by
renan.igor
• 0
1
vote
4
replies
500
views
cellranger error message
multiplexing
cellranger
updated 7 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
0
votes
6
replies
496
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 23 days ago by
gv
• 0 • written 6 weeks ago by
Srinka
▴ 20
5
votes
7
replies
488
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
Jacek
▴ 20
0
votes
6
replies
475
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 13 days ago by
swbarnes2
14k • written 14 days ago by
Erina
• 0
0
votes
2
replies
472
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
28 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
462
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
28 days ago by
Ashok
• 0
0
votes
8
replies
461
views
Error in cnetplot enrichplot package
R
updated 24 days ago by
Ram
43k • written 25 days ago by
Farhad
• 0
0
votes
5
replies
459
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 20 days ago by
Istvan Albert
100k • written 23 days ago by
sehriban.buyukkilic
▴ 10
1
vote
1
reply
454
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 26 days ago by
Gordon Smyth
★ 7.2k • written 29 days ago by
Chris
▴ 280
1
vote
1
reply
452
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 8 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
1
vote
3
replies
449
views
PCA plot
DESeq2
PCAplot
updated 19 days ago by
LauferVA
4.2k • written 22 days ago by
Aaliya
▴ 10
0
votes
5
replies
441
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 22 days ago by
GenoMax
142k • written 23 days ago by
Bertalan_Takacs
▴ 90
0
votes
2
replies
433
views
How can I solve this error?
metal
29 days ago by
22211020193
• 0
0
votes
5
replies
427
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
23 days ago by
njornet
▴ 20
0
votes
5
replies
425
views
Telescope issue
Telescope
RNA-seq
updated 16 days ago by
GenoMax
142k • written 17 days ago by
eleven11
• 0
0
votes
2
replies
420
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
28 days ago by
Ashok
• 0
0
votes
1
reply
418
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 29 days ago by
Ram
43k • written 20 months ago by
Muhammad
• 0
1
vote
4
replies
417
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 7 days ago by
GenoMax
142k • written 4 weeks ago by
aniigodwinn
• 0
0
votes
4
replies
415
views
Highest variable features in single cell data
single-cell
10 days ago by
carolofharvest
▴ 40
3
votes
7
replies
410
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
18 days ago by
salias
• 0
1
vote
6
replies
399
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 14 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
0
votes
4
replies
399
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 0
1
vote
9
replies
394
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 7 days ago by
i.sudbery
19k • written 10 days ago by
Assa Yeroslaviz
★ 1.8k
2
votes
4
replies
378
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
23 days ago by
samuelkalandarov2002
▴ 10
1
vote
3
replies
377
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 19 days ago by
ATpoint
82k • written 19 days ago by
Francesco
▴ 10
0
votes
2
replies
373
views
GSEA analysis in R
GSEA
R
Arabidopsis
29 days ago by
Sudip
• 0
0
votes
2
replies
366
views
How to update R on ubuntu
installation
update
R
apt-get
18 days ago by
Bosberg
▴ 50
0
votes
3
replies
363
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 18 days ago by
Ram
43k • written 5 months ago by
Fadi
• 0
1
vote
2
replies
358
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 4 days ago by
Ram
43k • written 5 days ago by
t.fortunato.asquini
• 0
1
vote
4
replies
345
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 4 days ago by
Vijith
▴ 30
0
votes
3
replies
343
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
3
replies
338
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 8 days ago by
bk11
★ 2.5k • written 12 days ago by
Yoosef
▴ 60
2
votes
2
replies
334
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 23 days ago by
Ram
43k • written 23 days ago by
v.berriosfarias
▴ 140
1
vote
3
replies
334
views
some error in building kraken2 database
metagenome
kraken2
23 days ago by
Art1ess
• 0
0
votes
0
replies
333
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
14 days ago by
NorbertK
▴ 10
3
votes
5
replies
331
views
Generating mpileup file using samtools
mpileup
samtools
updated 14 days ago by
Joe
21k • written 14 days ago by
Ruqaiya
• 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
23 days ago by
pramach1
▴ 40
1
vote
3
replies
325
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 16 days ago by
GenoMax
142k • written 17 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
324
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
12 days ago by
Lada
▴ 30
0
votes
1
reply
324
views
Could you please assist in identifying this cluster?
single-cell
updated 28 days ago by
Ram
43k • written 28 days ago by
carolofharvest
▴ 40
1
vote
2
replies
323
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
16 days ago by
Nafi
• 0
2
votes
3
replies
322
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 14 days ago by
dthorbur
★ 2.0k • written 14 days ago by
Vijith
▴ 30
0
votes
3
replies
322
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 17 days ago by
GenoMax
142k • written 18 days ago by
kim
• 0
0
votes
2
replies
321
views
bam merging for archaic samples
samtools
bam
updated 26 days ago by
Ram
43k • written 27 days ago by
Matteo Ungaro
▴ 100
0
votes
3
replies
321
views
KEGG Pathways
r
RNA-seq
updated 17 days ago by
Ram
43k • written 17 days ago by
Sudip
• 0
3
votes
4
replies
319
views
Truncated metadata file report from ENA Portal API
ena
python
7 days ago by
Giulia
• 0
347 results • Page
2 of 7
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
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Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
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16k
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Ezequiel
• 0
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alanh
▴ 170
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6.0k
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Recent Replies
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
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Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
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6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
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