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343 results • Page
2 of 7
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Votes
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0
votes
1
reply
149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 4 days ago by
Ram
43k • written 4 days ago by
eking28
• 0
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
4 days ago by
lagartija
▴ 160
0
votes
4
replies
258
views
Galaxy StringTie error
stringtie
galaxy
3 days ago by
trkfs
• 0
0
votes
0
replies
103
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
4 days ago by
atariw
▴ 10
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
1
reply
162
views
consensus sequence calling
consensus
updated 4 days ago by
bk11
★ 2.5k • written 4 days ago by
Ghada
• 0
0
votes
0
replies
88
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
4 days ago by
JACKY
▴ 140
0
votes
0
replies
102
views
Reference panel of normals for ensembl named refgenome
Mutect2
4 days ago by
gernophil
▴ 80
1
vote
0
replies
97
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
4 days ago by
tomas4482
▴ 400
3
votes
2
replies
189
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 4 days ago by
ATpoint
82k • written 4 days ago by
jennyp0706
• 0
0
votes
0
replies
110
views
lncRNA
tcga
lncrna
4 days ago by
jain72744
▴ 10
1
vote
2
replies
359
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
0
votes
2
replies
210
views
Output file of samtools flagstat empty
samtools-flagstat
updated 4 days ago by
colindaven
6.4k • written 5 days ago by
ramendra.sarma
• 0
0
votes
4
replies
401
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 0
0
votes
2
replies
231
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
4 days ago by
analyst
▴ 50
0
votes
1
reply
205
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 7 days ago by
Ram
43k • written 7 days ago by
Shwetha
• 0
0
votes
0
replies
165
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 7 days ago by
Ram
43k • written 7 days ago by
naomiboldon
• 0
1
vote
3
replies
285
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 7 days ago by
Ram
43k • written 7 days ago by
Omics data mining
▴ 260
0
votes
5
replies
318
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 days ago by
SilhouetteQ
• 0
0
votes
1
reply
190
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 7 days ago by
GenoMax
142k • written 7 days ago by
maria.soler
• 0
0
votes
2
replies
295
views
How are score_weights calculated in this code?
single-cell
6 days ago by
carolofharvest
▴ 40
0
votes
1
reply
224
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 7 days ago by
curious
▴ 750 • written 7 days ago by
SeoGyun
• 0
0
votes
0
replies
157
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
7 days ago by
Samantha
• 0
0
votes
1
reply
192
views
Microbial Signal Transduction Database
MiST
updated 7 days ago by
zx8754
11k • written 7 days ago by
Shravani
• 0
0
votes
0
replies
145
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
7 days ago by
singcell
• 0
0
votes
1
reply
219
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 7 days ago by
ATpoint
82k • written 7 days ago by
Amr
▴ 160
0
votes
2
replies
231
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
7 days ago by
jain72744
▴ 10
3
votes
1
reply
207
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 7 days ago by
dthorbur
★ 2.0k • written 7 days ago by
Eren
• 0
0
votes
0
replies
155
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
7 days ago by
Aytaç
• 0
0
votes
0
replies
171
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 7 days ago by
zx8754
11k • written 8 days ago by
curious_butterfly
• 0
0
votes
0
replies
163
views
supervised admixture
supervised
admixture
8 days ago by
RT
▴ 10
0
votes
2
replies
228
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 7 days ago by
Ram
43k • written 8 days ago by
sainavyav22
• 0
3
votes
4
replies
319
views
Truncated metadata file report from ENA Portal API
ena
python
7 days ago by
Giulia
• 0
0
votes
0
replies
189
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
8 days ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
156
views
input file for alternative splicing in rmats in linux
rmats
updated 8 days ago by
Ram
43k • written 8 days ago by
Lambodarswain316
• 0
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
0
replies
143
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
8 days ago by
Shae
▴ 10
1
vote
1
reply
162
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 8 days ago by
andres.firrincieli
3.6k • written 8 days ago by
kacollier
▴ 30
0
votes
0
replies
119
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 8 days ago by
Ram
43k • written 8 days ago by
curious_butterfly
• 0
1
vote
3
replies
265
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 8 days ago by
GenoMax
142k • written 9 days ago by
cput
• 0
0
votes
0
replies
121
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
9 days ago by
asalimih
▴ 60
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 9 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
0
votes
0
replies
108
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 9 days ago by
Ram
43k • written 9 days ago by
mathavanbioinfo
▴ 90
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
5
votes
7
replies
489
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
Jacek
▴ 20
0
votes
0
replies
147
views
Chance for trained without experience
bio
updated 9 days ago by
ATpoint
82k • written 9 days ago by
shehab
• 0
0
votes
0
replies
127
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
9 days ago by
Omics data mining
▴ 260
0
votes
2
replies
188
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
9 days ago by
njornet
▴ 20
0
votes
2
replies
216
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 9 days ago by
Adam
▴ 30 • written 9 days ago by
Darya
• 0
0
votes
5
replies
278
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 9 days ago by
Joe
21k • written 9 days ago by
Lemonhope
• 0
343 results • Page
2 of 7
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Answer: TFs and Gene databases
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Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
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alanh
▴ 170
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Recent Replies
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…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
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
Answer: 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.
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