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117,035 results • Page
1 of 2341
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Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 25 minutes ago by
GenoMax
142k • written 1 hour ago by
Bjorn
• 0
1
vote
4
replies
55
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 21 minutes ago by
Ram
43k • written 2 hours ago by
Harshita
• 0
2
votes
4
replies
74
views
Filter Genome for Specific Sites
bedtools
updated 20 minutes ago by
Ram
43k • written 2 hours ago by
Anita
• 0
0
votes
2
replies
124
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 20 minutes ago by
Ram
43k • written 18 hours ago by
Mohamed Samir
▴ 20
1
vote
1
reply
55
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 3 hours ago by
GenoMax
142k • written 4 hours ago by
niruf
• 0
0
votes
0
replies
35
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 13 minutes ago by
Ram
43k • written 4 hours ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
53
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
5 hours ago by
Biostar
2.8k
1
vote
3
replies
283
views
Super ehancers
enhancers
updated 4 hours ago by
GenoMax
142k • written 18 days ago by
Oburah
• 0
799
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
0
votes
0
replies
43
views
vcf phasing
beagle
WhatsHap
phasing
5 hours ago by
safeassli
▴ 10
0
votes
2
replies
122
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
2 hours ago by
sainavyav22
• 0
0
votes
1
reply
560
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 6 hours ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
136
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 3 hours ago by
Ram
43k • written 13 hours ago by
Sony
▴ 10
0
votes
3
replies
137
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 5 hours ago by
Ram
43k • written 9 hours ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
50
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 3 hours ago by
Ram
43k • written 9 hours ago by
ev97
▴ 20
0
votes
1
reply
90
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 7 hours ago by
marco.barr
▴ 130 • written 10 hours ago by
sooni
▴ 20
0
votes
1
reply
69
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 6 hours ago by
GenoMax
142k • written 10 hours ago by
jinyi
• 0
0
votes
0
replies
50
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
11 hours ago by
V_Vibes
• 0
0
votes
0
replies
75
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 22 minutes ago by
Ram
43k • written 11 hours ago by
JorgeVallejo
▴ 20
0
votes
0
replies
65
views
transcriptome annotation
annotation
trinity
transcriptome
updated 4 hours ago by
Ram
43k • written 12 hours ago by
Asim Bin Arshad
• 0
0
votes
5
replies
182
views
Why most genes have high padj values
RNA-seq
DEG
updated 3 hours ago by
Ram
43k • written 12 hours ago by
mnx0723
• 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 13 hours ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
93
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 13 hours ago by
ATpoint
82k • written 15 hours ago by
Pegasus
▴ 100
0
votes
1
reply
109
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 11 hours ago by
zx8754
11k • written 16 hours ago by
Ali
• 0
0
votes
4
replies
208
views
GO analysis: p-value range
GO
R
updated 9 hours ago by
Matthias Zepper
4.6k • written 20 hours ago by
sooni
▴ 20
1
vote
2
replies
90
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 13 minutes ago by
Ram
43k • written 20 hours ago by
Dr.
• 0
0
votes
3
replies
209
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 7 hours ago by
GenoMax
142k • written 1 day ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
77
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
21 hours ago by
Maryam
• 0
1
vote
7
replies
362
views
Add stats to the plot
R
updated 10 minutes ago by
Ram
43k • written 1 day ago by
Ghada
• 0
0
votes
4
replies
296
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
22 hours ago by
Bibi
• 0
1
vote
2
replies
330
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 23 hours ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
91
views
handling bio replicates for chromHMM
replicates
chromHMM
1 day ago by
Hasan_Daaboul
• 0
0
votes
0
replies
82
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
1 day ago by
DGTool
▴ 20
0
votes
1
reply
141
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 1 day ago by
ATpoint
82k • written 1 day ago by
rj.rezwan
• 0
0
votes
2
replies
293
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
1 day ago by
Ezequiel
• 0
2
votes
0
replies
165
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
1 day ago by
micah
▴ 30
0
votes
0
replies
100
views
problems in installing rDock
rDock
updated 10 minutes ago by
Ram
43k • written 1 day ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 1 day ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
705
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 1 day ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
1
reply
322
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
122
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
128
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
2 days ago by
Moinuddin
• 0
0
votes
1
reply
169
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Jacek
▴ 20
2
votes
1
reply
238
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 1 day ago by
Gordon Smyth
★ 7.2k • written 2 days ago by
marineandriot
• 0
0
votes
0
replies
131
views
How can i use ESM-1v ?
VEP
ESM-1v
2 days ago by
Meto
• 0
0
votes
0
replies
143
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Long
• 0
0
votes
3
replies
249
views
Trimming tool
Trimming
updated 11 minutes ago by
Ram
43k • written 3 days ago by
GeneC
• 0
0
votes
0
replies
139
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
3 days ago by
kilcdincer
▴ 10
0
votes
2
replies
255
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 2 days ago by
LauferVA
4.2k • written 3 days ago by
ijarne
• 0
0
votes
0
replies
161
views
genomic region of transcription factor
search
HOMER
motif
3 days ago by
qudrat.nii
▴ 10
117,035 results • Page
1 of 2341
Recent Votes
Answer: Kraken2 database
A: Why gene expression data should be log2 transformed?
Answer: Filter Genome for Specific Sites
Answer: Filter Genome for Specific Sites
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
The Biostar Herald for Monday, May 20, 2024
Answer: Generating Group/Cluster Lists from fastq files
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Recent Replies
Comment: Trimming tool
by
Ram
43k
Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
43k
This post does not fit the theme of this forum.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
43k
Hi, Congratulations but this is not LinkedIn, we are not a place to showcase your professional accomplishments. This does not fall under t…
Comment: Kraken2 Custom Database non-deterministic results
by
GenoMax
142k
Many (most?) programs related to NGS data analysis produce non-deterministic output (unless they explicitly offer an option to produce dete…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient?
by
Pedro
• 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
Comment: Filter Genome for Specific Sites
by
Anita
• 0
Great, thank you!
Comment: Filter Genome for Specific Sites
by
Anita
• 0
This is unhelpful and doesn't answer my question.
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
Thank you so much for helping me out in this! I have used most of the sequences that are found in this table. But, some samples like the…
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa This table has the SR…
Comment: Filter Genome for Specific Sites
by
Pierre Lindenbaum
161k
> My sites are in an Excel file right now ![enter image description here][1] <!-- was an American educator and academic administrator…
Answer: Filter Genome for Specific Sites
by
GenoMax
142k
> I have a list of ~1,300 single bp sites Convert your file to plain text [**BED format**][1] (three fields required). Use `bedtools slo…
Comment: How to generate an Upset plot in R to plot the shared variants between cell free
by
sainavyav22
• 0
It worked, Thank you very much!
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm unsure you'll be able to identify whole chromosomes that are not core from illumina reads alone. That might be easier to do with a micr…
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