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116,981 results • Page
1 of 2340
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News:
Course on Manual Genome Curation
GenomeAssembly
PretextView
Manual-Genome-Curation
24 minutes ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
100
views
Details on salmon index
Salmon
updated 47 minutes ago by
Rob
6.5k • written 7 hours ago by
Lorenzo
• 0
0
votes
0
replies
22
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
58 minutes ago by
Jsarria.EEAD
• 0
0
votes
1
reply
37
views
How can I calculate the OS of each patient?
overall-survival
updated 1 hour ago by
ATpoint
82k • written 1 hour ago by
Pedro
• 0
797
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
56
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 1 hour ago by
Ram
43k • written 3 hours ago by
m90
▴ 30
0
votes
0
replies
19
views
cat-bgen fail
bgenix
updated 1 hour ago by
Ram
43k • written 1 hour ago by
lambard
• 0
2
votes
4
replies
192
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
genome
updated 1 hour ago by
Ram
43k • written 9 hours ago by
Ali
• 0
3
votes
3
replies
76
views
getting exon coordinates
genomics
updated 1 hour ago by
Ram
43k • written 3 hours ago by
Xbox_27
• 0
1
vote
2
replies
73
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
Gabriel R.
★ 2.9k
0
votes
3
replies
177
views
How to extract cells of different species after mapping with combined genome?
snrnaseq
scrnaseq
updated 4 hours ago by
GenoMax
142k • written 18 hours ago by
vk
▴ 10
0
votes
5
replies
160
views
Can I perform a correlation test with 3 biological replicates per condition?
deseq2
RNA-Seq
correlation
gene
replicate
updated 3 hours ago by
ATpoint
82k • written 6 hours ago by
manuelmourato25
• 0
3
votes
4
replies
284
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 3 hours ago by
GenoMax
142k • written 6 hours ago by
Pierre Lindenbaum
161k
1
vote
8
replies
430
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 5 hours ago by
ATpoint
82k • written 1 day ago by
egascon
• 0
0
votes
0
replies
49
views
API kegg - IndexError: list index out of range
kegg
API
Error
7 hours ago by
mirwa.zidi93
• 0
0
votes
0
replies
45
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
8 hours ago by
Novogene
▴ 420
0
votes
0
replies
52
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
9 hours ago by
ebertomeup
• 0
0
votes
1
reply
92
views
Sam file Header problem
Sam
Header
problem
file
updated 9 hours ago by
Pierre Lindenbaum
161k • written 10 hours ago by
saifulislam99121
• 0
0
votes
4
replies
172
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
Degrees
python
Degree
offtopic
11 hours ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
510
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 12 hours ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
60
views
select set of intervals that cover a genomic region
GRanges
bed
12 hours ago by
ntsopoul
▴ 60
1
vote
0
replies
70
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
12 hours ago by
dwpeng
▴ 10
0
votes
0
replies
56
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
14 hours ago by
Luqman
• 0
1
vote
3
replies
153
views
ggrepel function: geom_text_repel()
ggrepel
ggplo2
R
8 hours ago by
sooni
▴ 20
0
votes
2
replies
124
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
10 hours ago by
mavy
▴ 10
1
vote
1
reply
179
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
19 hours ago by
ramiro.barrantes
• 0
1
vote
4
replies
212
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
9 minutes 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 19 hours ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
112
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 7 hours ago by
Michael
54k • written 20 hours ago by
mgranada3
▴ 30
0
votes
0
replies
72
views
Add line under stat test
stats
R
20 hours ago by
Ghada
• 0
1
vote
5
replies
760
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
72
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 22 hours ago by
GenoMax
142k • written 23 hours ago by
Rodolfo Adrián
• 0
1
vote
3
replies
160
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 22 hours ago by
Zhenyu Zhang
★ 1.2k • written 23 hours ago by
shpak.max
▴ 50
2
votes
4
replies
171
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
23 minutes ago by
ev97
▴ 20
0
votes
10
replies
327
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 20 minutes ago by
GenoMax
142k • written 1 day ago by
hophuquy0944
• 0
0
votes
4
replies
200
views
Sequencing Depth (Read Depth) Calculations
depth
14 hours ago by
LucisTheFather
• 0
0
votes
1
reply
109
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
1 day ago by
asalimih
▴ 60
0
votes
0
replies
81
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
1 day ago by
jway
• 0
2
votes
2
replies
150
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 2 hours ago by
Ram
43k • written 1 day ago by
jsmith120f
• 0
2
votes
2
replies
168
views
genome finishing
finishing
genome
updated 1 day ago by
nd48
▴ 20 • written 1 day ago by
trezini
• 0
1
vote
5
replies
190
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
biology_inform
▴ 50
1
vote
4
replies
258
views
Add stats to boxplot in R
stats
R
22 hours ago by
Ghada
• 0
0
votes
1
reply
125
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 5 hours ago by
Papyrus
★ 2.9k • written 1 day ago by
yura.grabovska
▴ 90
0
votes
1
reply
108
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 2 hours ago by
GenoMax
142k • written 1 day ago by
Lélé
▴ 10
0
votes
4
replies
228
views
calculating genomic coverage/ base overlap in R
genomics
updated 2 hours ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
1
vote
5
replies
216
views
Annotating file using bcftools
annotation
plink
bcftools
2 hours ago by
kl
▴ 10
0
votes
9
replies
325
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
10 hours ago by
njornet
▴ 20
0
votes
3
replies
144
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
1 day ago by
Esraa
• 0
3
votes
3
replies
207
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 8 hours ago by
ATpoint
82k • written 1 day ago by
Alexandra
• 0
1
vote
1
reply
208
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 1 day ago by
dariober
14k • written 2 days ago by
Holly
▴ 10
116,981 results • Page
1 of 2340
Recent Votes
Answer: Probe annotation file for microarray platform MoGene-1_0-st-v1
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
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Recent Awards •
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carlopecoraro2
★ 2.5k
Scholar
to
GenoMax
142k
Popular Question
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ben@f
▴ 20
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Jalil Sharif
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Recent Replies
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.
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…
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