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117,001 results • Page
4 of 2341
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
402
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 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
0
votes
2
replies
232
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
4 days ago by
analyst
▴ 50
0
votes
6
replies
421
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 4 days ago by
Ram
43k • written 7 days ago by
ajbarrett98
• 0
0
votes
11
replies
543
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
5 days ago by
Tuck898
• 0
3
votes
3
replies
282
views
what is another word for a BLAST "hit"?
blast
alignment
7 days ago by
dec986
▴ 380
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
287
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
9
votes
6
replies
12k
views
samtools tview symbols
samtools
updated 8.8 years ago by
Ashutosh Pandey
12k • written 8.8 years ago by
biolab
★ 1.4k
2
votes
9
replies
696
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 10 days ago by
schmince
• 0
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
191
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
296
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
1
vote
1
reply
218
views
DESeq2 error
DESeq2
updated 7 days ago by
ATpoint
82k • written 8 days ago by
sooni
▴ 20
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
6
votes
2
replies
240
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 7 days ago by
Gordon Smyth
★ 7.2k • written 8 days ago by
gBioStar5
▴ 10
2
votes
5
replies
410
views
Importing a fastq file
Fastq
updated 8 days ago by
size_t
▴ 120 • written 8 days ago by
oumo
• 0
3
votes
1
reply
207
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 7 days ago by
dthorbur
★ 2.0k • written 8 days ago by
Eren
• 0
0
votes
0
replies
156
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
8 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
2
votes
0
replies
155
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
8 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
456
views
Different output for read length
samtools
BAM
8 days ago by
marco.barr
▴ 130
0
votes
1
reply
367
views
Snakemake fails to find conda in PBS
snakemake
updated 8 days ago by
tim.booth
▴ 60 • written 5 weeks ago by
yixinzeng
• 0
0
votes
2
replies
230
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
3
replies
564
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 8 days ago by
Ram
43k • written 12 weeks ago by
maplewj
▴ 10
0
votes
5
replies
332
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
5 days ago by
feather-W
• 0
0
votes
3
replies
301
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 8 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
Matthew
• 0
3
votes
4
replies
3.0k
views
Have you ever obtained user guide of ExomeCNV?
CNV
updated 4.4 years ago by
lffu_0032
▴ 90 • written 5.2 years ago by
oghzzang
▴ 50
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
2
votes
2
replies
249
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 8 days ago by
Michael
54k • written 8 days ago by
ashaneev07
▴ 20
1
vote
1
reply
453
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
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 8 days ago by
Pierre Lindenbaum
161k • written 8 days ago by
Lila M
★ 1.2k
2
votes
3
replies
234
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 8 days ago by
Pierre Lindenbaum
161k • written 8 days ago by
ScottDansk
▴ 10
1
vote
0
replies
143
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
8 days ago by
Shae
▴ 10
0
votes
1
reply
195
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 8 days ago by
marco.barr
▴ 130 • written 9 days ago by
odi
▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 8 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 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
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 8 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
119
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 9 days ago by
Ram
43k • written 9 days ago by
curious_butterfly
• 0
1
vote
4
replies
341
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 4 days ago by
Ram
43k • written 9 days ago by
samRayne
• 0
1
vote
3
replies
269
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 8 days ago by
GenoMax
142k • written 9 days ago by
cput
• 0
117,001 results • Page
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Recent Replies
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…
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: 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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