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50 results • Page
1 of 1
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Rank
Views
Votes
Replies
0
votes
0
replies
10
views
Use of ichor CNA
Dog
CNA
genome
31 minutes ago by
sainavyav22
• 0
2
votes
1
reply
40
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
cell
RNA
single
ambient
updated 36 minutes ago by
e.r.zakiev
▴ 210 • written 1 hour ago by
txema.heredia
▴ 130
0
votes
0
replies
25
views
News:
Course on Manual Genome Curation
GenomeAssembly
PretextView
Manual-Genome-Curation
2 hours ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
122
views
Details on salmon index
Salmon
updated 2 hours ago by
Rob
6.5k • written 9 hours ago by
Lorenzo
• 0
0
votes
0
replies
33
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
3 hours ago by
Jsarria.EEAD
• 0
0
votes
1
reply
68
views
How can I calculate the OS of each patient?
overall-survival
updated 3 hours ago by
ATpoint
82k • written 3 hours ago by
Pedro
• 0
0
votes
1
reply
76
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 3 hours ago by
Ram
43k • written 6 hours ago by
m90
▴ 30
0
votes
0
replies
34
views
cat-bgen fail
bgenix
updated 3 hours ago by
Ram
43k • written 4 hours ago by
lambard
• 0
2
votes
4
replies
207
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
genome
updated 3 hours ago by
Ram
43k • written 11 hours ago by
Ali
• 0
3
votes
3
replies
108
views
getting exon coordinates
genomics
updated 4 hours ago by
Ram
43k • written 5 hours ago by
Xbox_27
• 0
1
vote
2
replies
92
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
Gabriel R.
★ 2.9k
0
votes
3
replies
183
views
How to extract cells of different species after mapping with combined genome?
snrnaseq
scrnaseq
updated 6 hours ago by
GenoMax
142k • written 20 hours ago by
vk
▴ 10
0
votes
5
replies
175
views
Can I perform a correlation test with 3 biological replicates per condition?
deseq2
RNA-Seq
correlation
gene
replicate
updated 5 hours ago by
ATpoint
82k • written 8 hours ago by
manuelmourato25
• 0
3
votes
4
replies
300
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 5 hours ago by
GenoMax
142k • written 9 hours ago by
Pierre Lindenbaum
161k
1
vote
8
replies
443
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
updated 7 hours ago by
ATpoint
82k • written 1 day ago by
egascon
• 0
0
votes
0
replies
53
views
API kegg - IndexError: list index out of range
kegg
API
Error
9 hours ago by
mirwa.zidi93
• 0
0
votes
0
replies
49
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
11 hours ago by
Novogene
▴ 420
0
votes
0
replies
57
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
11 hours ago by
ebertomeup
• 0
0
votes
1
reply
99
views
Sam file Header problem
Sam
Header
problem
file
updated 11 hours ago by
Pierre Lindenbaum
161k • written 12 hours ago by
saifulislam99121
• 0
0
votes
4
replies
178
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
Degrees
python
Degree
offtopic
13 hours ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
515
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 14 hours ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
66
views
select set of intervals that cover a genomic region
GRanges
bed
14 hours ago by
ntsopoul
▴ 60
1
vote
0
replies
76
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
14 hours ago by
dwpeng
▴ 10
0
votes
0
replies
60
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
16 hours ago by
Luqman
• 0
1
vote
3
replies
159
views
ggrepel function: geom_text_repel()
ggrepel
ggplo2
R
10 hours ago by
sooni
▴ 20
0
votes
2
replies
129
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
12 hours ago by
mavy
▴ 10
1
vote
1
reply
184
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
21 hours ago by
ramiro.barrantes
• 0
1
vote
4
replies
246
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
2 hours ago by
diqixiaoyaoer
▴ 10
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 21 hours ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
117
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 9 hours ago by
Michael
54k • written 22 hours ago by
mgranada3
▴ 30
0
votes
0
replies
77
views
Add line under stat test
stats
R
23 hours ago by
Ghada
• 0
2
votes
4
replies
206
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
2 hours ago by
ev97
▴ 20
1
vote
12
replies
386
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
1 hour ago by
hophuquy0944
• 0
0
votes
4
replies
204
views
Sequencing Depth (Read Depth) Calculations
depth
16 hours ago by
LucisTheFather
• 0
2
votes
2
replies
153
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 4 hours ago by
Ram
43k • written 1 day ago by
jsmith120f
• 0
0
votes
1
reply
129
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 7 hours ago by
Papyrus
★ 2.9k • written 1 day ago by
yura.grabovska
▴ 90
0
votes
1
reply
123
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 4 hours ago by
GenoMax
142k • written 1 day ago by
Lélé
▴ 10
0
votes
4
replies
232
views
calculating genomic coverage/ base overlap in R
genomics
updated 4 hours ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
1
vote
5
replies
230
views
Annotating file using bcftools
annotation
plink
bcftools
4 hours ago by
kl
▴ 10
0
votes
9
replies
330
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
12 hours ago by
njornet
▴ 20
3
votes
3
replies
212
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 9 hours ago by
ATpoint
82k • written 1 day ago by
Alexandra
• 0
1
vote
4
replies
263
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
21 hours ago by
Arton
▴ 10
0
votes
5
replies
272
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 17 hours ago by
GenoMax
142k • written 1 day ago by
chrisk
• 0
0
votes
2
replies
159
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 7 hours ago by
DGTool
▴ 20 • written 1 day ago by
iqra
• 0
1
vote
2
replies
207
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
22 hours ago by
MarcosCosta
• 0
1
vote
2
replies
198
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
2 hours ago by
bioinfo
▴ 150
0
votes
2
replies
215
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
20 hours ago by
Chen
• 0
1
vote
3
replies
229
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 46 minutes ago by
GenoMax
142k • written 2 days ago by
ohtang7
▴ 40
0
votes
9
replies
594
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
21 hours ago by
Arton
▴ 10
1
vote
3
replies
763
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 18 minutes ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
50 results • Page
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Recent Votes
Answer: --normalizeUsing RPGC
Answer: Details on salmon index
Answer: Details on salmon index
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
A: How count reads
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Popular Question
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carlopecoraro2
★ 2.5k
Scholar
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GenoMax
142k
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ben@f
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Recent Replies
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly
by
sansan_96
▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
e.r.zakiev
▴ 210
Very good question and analysis. I personally only tried SoupX so can't weigh in on the comparison. This might be not really the issue here…
Comment: Is there any way to modify this pie chart ?
by
marco.barr
▴ 120
Try following the same logic as the guide which adds the labels about halfway through each pie slice value. Check column's name in script b…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
sorry for that, this is first time i use it.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank sir, i will check it again
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
Ok, I will response to you here as soon as possible.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
How much memory do you have available? For `nt` database you are going to need 30-40G minimum. You may simply be running out of memory.
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.
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