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397 results • Page
5 of 8
Sort: Views
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Views
Votes
Replies
0
votes
1
reply
230
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 14 days ago by
GenoMax
142k • written 14 days ago by
mgranada3
▴ 30
0
votes
0
replies
229
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
24 days ago by
Javier
• 0
0
votes
1
reply
228
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 29 days ago by
DKA
▴ 40 • written 29 days ago by
james.melhorn
• 0
0
votes
2
replies
228
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
13 days ago by
dtnondorf
• 0
0
votes
2
replies
227
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
3 days ago by
analyst
▴ 50
0
votes
2
replies
227
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
6 days ago by
jain72744
▴ 10
0
votes
2
replies
226
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 7 days ago by
swbarnes2
14k • written 9 days ago by
ahmad.sajad4541
• 0
0
votes
2
replies
226
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 5 days ago by
Ram
43k • written 7 days ago by
sainavyav22
• 0
0
votes
0
replies
225
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 27 days ago by
Ram
43k • written 27 days ago by
Dinmukhamed
• 0
0
votes
0
replies
224
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
20 days ago by
HarperReed
• 0
0
votes
0
replies
222
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 23 days ago by
Ram
43k • written 23 days ago by
Pine
▴ 20
0
votes
1
reply
222
views
Freyja plot error
Freyja
updated 29 days ago by
Ram
43k • written 29 days ago by
Adyasha
• 0
0
votes
1
reply
221
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 5 days ago by
curious
▴ 750 • written 6 days ago by
SeoGyun
• 0
0
votes
0
replies
219
views
Lncipedia GTF file error
Proteomics
updated 27 days ago by
Ram
43k • written 27 days ago by
atharvakarkare14
▴ 30
0
votes
1
reply
215
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 6 days ago by
ATpoint
82k • written 6 days ago by
Amr
▴ 160
0
votes
0
replies
215
views
miRDeep2: How to get the read counts
mirdeep2
27 days ago by
Atul K.
• 0
0
votes
0
replies
214
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
28 days ago by
synat.keam
▴ 100
0
votes
1
reply
213
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 12 days ago by
Ram
43k • written 12 days ago by
Valentina
• 0
0
votes
2
replies
213
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
8 days ago by
Nicholas
• 0
1
vote
1
reply
213
views
Failed kmer content
kmer
illumina
ngs
updated 23 days ago by
Ram
43k • written 23 days ago by
Kasturi
• 0
0
votes
1
reply
212
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 23 days ago by
bk11
★ 2.4k • written 23 days ago by
Susmita Mandal
▴ 110
0
votes
2
replies
212
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 8 days ago by
Adam
▴ 30 • written 8 days ago by
Darya
• 0
0
votes
1
reply
212
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 22 days ago by
bk11
★ 2.4k • written 22 days ago by
alphaflylizard
• 0
0
votes
0
replies
210
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
28 days ago by
enferdeflame
• 0
0
votes
0
replies
209
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 26 days ago by
Ram
43k • written 26 days ago by
mja
• 0
0
votes
0
replies
209
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
27 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
208
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 23 days ago by
GenoMax
142k • written 23 days ago by
Srinka
▴ 20
0
votes
1
reply
207
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 22 days ago by
Sofia
• 0 • written 22 days ago by
mawigoj318
• 0
0
votes
0
replies
207
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
26 days ago by
Nitin
• 0
3
votes
1
reply
206
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 6 days ago by
dthorbur
★ 2.0k • written 6 days ago by
Eren
• 0
0
votes
1
reply
202
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 5 days ago by
Ram
43k • written 5 days ago by
Shwetha
• 0
0
votes
2
replies
202
views
Output file of samtools flagstat empty
samtools-flagstat
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
ramendra.sarma
• 0
0
votes
1
reply
202
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 15 days ago by
i.sudbery
19k • written 15 days ago by
Edmond
• 0
0
votes
0
replies
201
views
Chemical structure validation
structure
cap
validation
metabolite
26 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
199
views
RNA-seq bacteria contamination
RNA-seq
updated 24 days ago by
GenoMax
142k • written 24 days ago by
sh
• 0
0
votes
1
reply
197
views
Differential Accessibility
DiffBind
updated 16 days ago by
Ram
43k • written 16 days ago by
Shloka
• 0
0
votes
0
replies
196
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
20 days ago by
simplitia
▴ 130
0
votes
3
replies
196
views
How to access GWAVA software of data
GWAVA
updated 2 days ago by
GenoMax
142k • written 2 days ago by
nonaddldy
▴ 10
0
votes
0
replies
196
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
28 days ago by
P.
• 0
0
votes
0
replies
195
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
29 days ago by
Ali
• 0
1
vote
0
replies
192
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
20 days ago by
rohitsatyam102
▴ 860
0
votes
0
replies
192
views
RNA-seq: full length gene
RNA-seq
updated 20 days ago by
Ram
43k • written 20 days ago by
Nargis
• 0
0
votes
0
replies
191
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 19 days ago by
Ram
43k • written 20 days ago by
SineWave
• 0
0
votes
2
replies
189
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
17 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
189
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 22 days ago by
Mensur Dlakic
★ 27k • written 22 days ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
189
views
Microbial Signal Transduction Database
MiST
updated 6 days ago by
zx8754
11k • written 6 days ago by
Shravani
• 0
0
votes
0
replies
188
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
7 days ago by
Matvii Mykhailichenko
• 0
1
vote
2
replies
188
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
9 days ago by
robert.flynn.21
• 0
0
votes
0
replies
187
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 28 days ago by
GenoMax
142k • written 29 days ago by
srimmer
• 0
0
votes
2
replies
187
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
8 days ago by
njornet
▴ 20
397 results • Page
5 of 8
Recent Votes
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
C: Splitting .vcf file
Answer: Grouping datasets in Seurat
Answer: How should I make kallisto indexes?
Comment: Why does assigning genes with biomart give me different values than using a tran
Answer: Grouping datasets in Seurat
Best tool to find potential TF binding sites within a specific DNA sequence?
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142k
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Recent Replies
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Noted! Thanks very much for your help!
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i'm using linux. I was use 3 file.fasta to debug and it is nucleotide file, and my blast -h still work > (/data/quyho/tools/mgs2amr_tool…
Answer: Details on salmon index
by
Rob
6.5k
Hi Lorenzo, Thanks for your question. First, I'd like to clarify that several substantial updates have been made to salmon since its …
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 90
sc/snRNASeq tends to have differences in things like mitochondrial genes etc, which you can account for using tools like SCTransform but in…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
bioinfo
▴ 150
Thank you! I ended up using the transcripts_to_genes instead of biomart.
Comment: How can I calculate the OS of each patient?
by
ATpoint
82k
Please be specific. Which TCGA subset, what did you try? Show code.
Answer: mitochondrial genome assembly pipeline
by
shelkmike
★ 1.2k
A good tool for mitochondrial genome assembly is GetOrganelle (https://github.com/Kinggerm/GetOrganelle)
Comment: getting exon coordinates
by
Ram
43k
Please do not use `bioinformatics` as a tag unless your post in about the field of bioinformatics itself.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
I've removed unneccessary tags - `meta` and `how-to` don't apply to this post at all, and the `forum` tag is not in use anymore.
Comment: Difference in number of reads when using duplex and simplex base calling with Do
by
GenoMax
142k
I assume you have posted this in nanopore community and/or on the dorado issues page on GitHub. Please come back and post an update once yo…
Comment: Annotating file using bcftools
by
kl
▴ 10
Do you know if there is a way to leave chr:pos in ID if there is no matching rsid based on chromosome and position, as variants have been r…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
Jeremy Leipzig
22k
We get this question like clockwork every 6 weeks. I'll say it one more time: **A freeze is a freeze.** Patches are not a thing th…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Thanks very much for your feedback! I will take all those things in consideration once I start the analysis! Just out of curiosity, do yo…
Answer: getting exon coordinates
by
ben@f
▴ 20
A combination of bash and awk can do the work, suppose you have the gff file annotation of your gene of interest and a text file with Gene…
Comment: getting exon coordinates
by
Pierre Lindenbaum
161k
https://www.biostars.org/p/385786/ ; <br> https://www.biostars.org/p/276608/ ; <br> https://www.biostars.org/p/411934/ ;etc... <!-- How …
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