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760 results • Page
4 of 16
Sort: replies
Rank
Views
Votes
Replies
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 5 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
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
1
vote
5
replies
808
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 28 days ago by
BioinfGuru
★ 1.7k • written 29 days ago by
rrehimi
• 0
2
votes
5
replies
954
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 18 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
2
votes
5
replies
787
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 27 days ago by
Jesse
▴ 770 • written 28 days ago by
Ann
★ 2.4k
0
votes
5
replies
383
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 13 days ago by
chrchang523
10k • written 14 days ago by
curious
▴ 750
8
votes
5
replies
6.5k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
3
votes
5
replies
395
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
14 days ago by
Maverick
▴ 10
1
vote
5
replies
493
views
How should I make kallisto indexes?
kallisto
updated 18 days ago by
dsull
★ 6.0k • written 4 weeks ago by
bioinfo
▴ 150
0
votes
5
replies
325
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
9 days ago by
me
• 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
2
votes
5
replies
268
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 3 days ago by
Philipp Bayer
8.5k • written 3 days ago by
林明德
• 0
3
votes
5
replies
636
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
25 days ago by
n_navy
• 0
2
votes
5
replies
493
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 3 days ago by
Ram
43k • written 9 days ago by
Prawesh
• 0
0
votes
4
replies
244
views
calculating genomic coverage/ base overlap in R
genomics
updated 1 day ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 4 days ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
3
votes
4
replies
268
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 6 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
Ali
• 0
3
votes
4
replies
418
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
22 days ago by
QX
• 0
1
vote
4
replies
282
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 days ago by
Arton
▴ 10
2
votes
4
replies
2.7k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 18 days ago by
Medhat
9.7k • written 2.0 years ago by
Vitor1
▴ 120
1
vote
4
replies
389
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
10 days ago by
heelpPlease
• 0
1
vote
4
replies
340
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 4 days ago by
Ram
43k • written 8 days ago by
samRayne
• 0
3
votes
4
replies
542
views
biomaRt error for different R version
biomaRt
R
updated 29 days ago by
GenoMax
142k • written 4 weeks ago by
manaswwm
▴ 510
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
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
238
views
Sequencing Depth (Read Depth) Calculations
depth
1 day ago by
LucisTheFather
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 29 days ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 3 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
293
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
2 days ago by
Esraa
• 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 6 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
2
votes
4
replies
269
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 2 days ago by
yura.grabovska
▴ 90 • written 2 days ago by
ev97
▴ 20
5
votes
4
replies
716
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
23 days ago by
kirillkirilenko
▴ 40
1
vote
4
replies
388
views
Segmentation error while using a tool
smalt
updated 13 days ago by
Mensur Dlakic
★ 27k • written 13 days ago by
Ruqaiya
• 0
0
votes
4
replies
255
views
Merge clusters in Seurat UMAP
seurat
umap
13 hours ago by
kilcdincer
▴ 10
1
vote
4
replies
501
views
cellranger error message
multiplexing
cellranger
updated 7 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
0
votes
4
replies
303
views
Genbank File Format
gbkformat
17 days ago by
alenew.am
• 0
3
votes
4
replies
747
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
25 days ago by
rahu
• 0
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 29 days ago by
Ram
43k • written 5.1 years ago by
georgians
▴ 50
0
votes
4
replies
335
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 17 days ago by
Ram
43k • written 17 days ago by
Hamtaro
▴ 50
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 22 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
15 days ago by
eebloom
▴ 80
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 9 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
0
votes
4
replies
622
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 27 days ago by
ATpoint
82k • written 28 days ago by
rheab1230
▴ 140
0
votes
4
replies
662
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
28 days ago by
Kai Xin
• 0
0
votes
4
replies
586
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
29 days ago by
feather-W
• 0
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 29 days ago by
Ram
43k • written 7.5 years ago by
Tenghui Chen
• 0
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 29 days ago by
Ram
43k • written 2.3 years ago by
claysandel
• 0
1
vote
4
replies
284
views
Add stats to boxplot in R
stats
R
2 days ago by
Ghada
• 0
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 29 days ago by
Ram
43k • written 7.2 years ago by
dyollluap
▴ 310
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 29 days ago by
Ram
43k • written 7.2 years ago by
hellocita
▴ 40
760 results • Page
4 of 16
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Recent Replies
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Comment: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
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
Zhenyu Zhang
★ 1.2k
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.
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