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315 results • Page
2 of 7
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Views
Votes
Replies
0
votes
0
replies
113
views
Is there a real ground truth for CNV data?
CNV
5 days ago by
jennyp0706
• 0
1
vote
1
reply
148
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 4 days ago by
Ram
43k • written 5 days ago by
kilcdincer
▴ 10
0
votes
3
replies
209
views
How to access GWAVA software of data
GWAVA
updated 5 days ago by
GenoMax
142k • written 5 days ago by
nonaddldy
▴ 10
0
votes
0
replies
95
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
5 days ago by
Spring
• 0
0
votes
2
replies
187
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
5 days ago by
IdaHao0921
• 0
0
votes
3
replies
355
views
Snakemake wrapper issue
fastqc
snakemake
updated 5 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
162
views
How to process Bulk WES data?
WES
WGS
updated 5 days ago by
GenoMax
142k • written 5 days ago by
wyuan37
• 0
0
votes
1
reply
162
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 5 days ago by
GenoMax
142k • written 5 days ago by
cedric.blais
• 0
0
votes
1
reply
152
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 5 days ago by
Ram
43k • written 5 days ago by
eking28
• 0
0
votes
0
replies
105
views
reference-free assembly error assessment tools
assembly
5 days ago by
lagartija
▴ 160
0
votes
4
replies
263
views
Galaxy StringTie error
stringtie
galaxy
5 days ago by
trkfs
• 0
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
6 days ago by
atariw
▴ 10
1
vote
4
replies
352
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 days ago by
Juke34
8.6k • written 6 days ago by
Vijith
▴ 30
0
votes
1
reply
165
views
consensus sequence calling
consensus
updated 6 days ago by
bk11
★ 2.5k • written 6 days ago by
Ghada
• 0
0
votes
0
replies
89
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
6 days ago by
JACKY
▴ 140
0
votes
0
replies
104
views
Reference panel of normals for ensembl named refgenome
Mutect2
6 days ago by
gernophil
▴ 80
1
vote
0
replies
99
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
6 days ago by
tomas4482
▴ 400
3
votes
2
replies
199
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 6 days ago by
ATpoint
82k • written 6 days ago by
jennyp0706
• 0
0
votes
0
replies
112
views
lncRNA
tcga
lncrna
6 days ago by
jain72744
▴ 10
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 6 days ago by
Ram
43k • written 7 days ago by
t.fortunato.asquini
• 0
0
votes
2
replies
215
views
Output file of samtools flagstat empty
samtools-flagstat
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
ramendra.sarma
• 0
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
6 days ago by
beginner123
• 0
0
votes
2
replies
235
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
6 days ago by
analyst
▴ 50
0
votes
1
reply
207
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 8 days ago by
Ram
43k • written 8 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 8 days ago by
Ram
43k • written 9 days ago by
naomiboldon
• 0
1
vote
3
replies
294
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 9 days ago by
Omics data mining
▴ 260
0
votes
5
replies
326
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
6 days ago by
SilhouetteQ
• 0
0
votes
1
reply
197
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 9 days ago by
GenoMax
142k • written 9 days ago by
maria.soler
• 0
0
votes
2
replies
301
views
How are score_weights calculated in this code?
single-cell
8 days ago by
carolofharvest
▴ 40
0
votes
1
reply
228
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 8 days ago by
curious
▴ 750 • written 9 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
9 days ago by
Samantha
• 0
0
votes
1
reply
194
views
Microbial Signal Transduction Database
MiST
updated 9 days ago by
zx8754
11k • written 9 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
9 days ago by
singcell
• 0
0
votes
1
reply
220
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 9 days ago by
ATpoint
82k • written 9 days ago by
Amr
▴ 160
0
votes
2
replies
235
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
9 days ago by
jain72744
▴ 10
3
votes
1
reply
209
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 9 days ago by
dthorbur
★ 2.0k • written 9 days ago by
Eren
• 0
0
votes
0
replies
158
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
9 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 9 days ago by
zx8754
11k • written 9 days ago by
curious_butterfly
• 0
0
votes
0
replies
165
views
supervised admixture
supervised
admixture
9 days ago by
RT
▴ 10
0
votes
2
replies
231
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 8 days ago by
Ram
43k • written 10 days ago by
sainavyav22
• 0
3
votes
4
replies
330
views
Truncated metadata file report from ENA Portal API
ena
python
8 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
10 days ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
157
views
input file for alternative splicing in rmats in linux
rmats
updated 10 days ago by
Ram
43k • written 10 days ago by
Lambodarswain316
• 0
1
vote
1
reply
458
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 10 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
10 days ago by
Shae
▴ 10
1
vote
1
reply
163
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 10 days ago by
andres.firrincieli
3.6k • written 10 days ago by
kacollier
▴ 30
0
votes
0
replies
119
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 10 days ago by
Ram
43k • written 10 days ago by
curious_butterfly
• 0
1
vote
4
replies
320
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
Joe
21k • written 10 days ago by
cput
• 0
0
votes
0
replies
122
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
10 days ago by
asalimih
▴ 60
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 10 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
315 results • Page
2 of 7
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
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?
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★ 2.5k
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▴ 30
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Recent Replies
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
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.…
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