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120,529 results • Page
1 of 2411
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0
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6
views
Potential mapping issues in Cas9 knockout cells with STAR (the truncated RNA)
STAR
RNA-seq
15 minutes ago by
Weize
• 0
0
votes
0
replies
17
views
Normalizing Peaks in ChIP seq
seq
ChIP
1 hour ago by
mropri
▴ 160
0
votes
0
replies
28
views
Minimal Quality Control Thresholds in Shotgun or Amplicon Metagenomics for non assembly based analysis
QC
Microbiome
fastp
3 hours ago by
Maxwell
▴ 50
0
votes
1
reply
47
views
NCBI genome submission validation error
genome
annotation
updated 3 hours ago by
lieven.sterck
15k • written 4 hours ago by
slin023
• 0
0
votes
0
replies
29
views
Estimating the Relative Abundance of a Species in a Mixed Microbial Community Using 16S PCR
16S
4 hours ago by
ljrdain2508
• 0
828
votes
169
replies
168k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
2
votes
2
replies
94
views
Training Augustus for Gene Prediction
Augustus
Busco
genome
prediction
gene
updated 4 hours ago by
Buffo
★ 2.4k • written 6 hours ago by
shiv
▴ 10
0
votes
1
reply
87
views
Mus musculus genome scaffold discrepancy
genome
ncbi
updated 7 hours ago by
Wayne
★ 2.1k • written 10 hours ago by
SJP
• 0
0
votes
1
reply
65
views
Edit Dataset FASTQ files using ReadStore Command Line Interface
FASTQ
Readstore
CLI
updated 9 hours ago by
ATpoint
87k • written 9 hours ago by
DNAStar
• 0
0
votes
0
replies
45
views
plyranges – joining gpos object only by the start coordinate of the range
GenomicRanges
plyranges
updated 9 hours ago by
Pierre Lindenbaum
165k • written 9 hours ago by
Kateřina
• 0
0
votes
1
reply
74
views
Fast querying of variant metrics with database
python
database
updated 10 hours ago by
Pierre Lindenbaum
165k • written 10 hours ago by
DBScan
▴ 470
2
votes
1
reply
85
views
Mitochondrial Variant Calling Tools
Mitochondrial
NGS
Variant
Calling
Illumina
updated 10 hours ago by
Pierre Lindenbaum
165k • written 11 hours ago by
adarsh_munna
▴ 60
1
vote
3
replies
463
views
How to use harmony with scanpy?
scanpy
harmony
updated 11 hours ago by
Rezin
• 0 • written 14 days ago by
bioinfo
▴ 150
1
vote
2
replies
97
views
SpliceAI custom gene annotation file
GENCODE
SpliceAI
9 hours ago by
ClkElf
▴ 50
0
votes
0
replies
66
views
Job:
Postdoc in Reproductive genetics - bioinformatics
Sweden
bioinformatics
genetics
postdoc
12 hours ago by
pol.sole.navais
• 0
0
votes
0
replies
86
views
What is a recommended maximum read depth threshold for DNA variant filtration, supported by scientific articles?
filtering
articles-search
read-depth
variant-calling
13 hours ago by
Sofya
• 0
9
votes
13
replies
2.4k
views
How are probabilities of insertions and deletions encoded in FASTQ?
fastq
phred quality score
nanopore
pacbio
indels
updated 2 hours ago by
Jeremy Leipzig
23k • written 6.0 years ago by
shelkmike
★ 1.5k
0
votes
2
replies
118
views
samtools mpileup and samtools tview give different reads quality results
samtools
tview
mpileup
15 hours ago by
cocoboxt
• 0
9
votes
12
replies
7.2k
views
picard installation failure
error
software
picard
updated 16 hours ago by
lieven.sterck
15k • written 7.5 years ago by
sanariyaz21
• 0
0
votes
1
reply
113
views
low alignment rate for RNA-Seq data
rice
low
alignment
RNA-Seq
updated 17 hours ago by
michael.ante
★ 4.0k • written 19 hours ago by
analyst
▴ 60
2
votes
1
reply
112
views
Optimal Computer Configuration for Bioinformatics Analysis
scRNA-seq
computer
updated 16 hours ago by
ATpoint
87k • written 20 hours ago by
Song
▴ 10
0
votes
1
reply
132
views
Variant Missing in VCF but Present in BAM Files: Discrepancy Identified via IGV Report in Join-Call Project
GATK
Deepvariant
BWA
updated 19 hours ago by
Pierre Lindenbaum
165k • written 23 hours ago by
lunping98
• 0
0
votes
0
replies
75
views
no "-" strand in transcriptome alignment
DRS
transcriptome
alignment
10 hours ago by
baibhu1234
▴ 20
0
votes
0
replies
73
views
Anndata vs cloupe
seurat
cloupe
scanpy
anndata
1 day ago by
Rika
• 0
0
votes
3
replies
160
views
Gene Mapping Issue
DAVID
updated 16 hours ago by
lieven.sterck
15k • written 1 day ago by
won
• 0
0
votes
0
replies
95
views
Job:
Assistant, Associate, or Full Project Scientist in Molecular Biology
molecular
teaching
biology
1 day ago by
UCSDBioSci
▴ 30
2
votes
4
replies
206
views
RNA variant calling - SNP and indels files
mouse
variant_calling
genomics
RNA
12 hours ago by
Nerelys
• 0
2
votes
4
replies
189
views
Manta analysis in WES
Deletion
MANTA
WES
SV
Exomiser
1 day ago by
Eduardo
• 0
0
votes
1
reply
108
views
All VS All contamination check for tumor samples
tumor
contamination
18 hours ago by
mps
• 0
1
vote
2
replies
148
views
Determine binding sites in unstimulated TF ChIP-seq samples
ChIP-seq
csaw
1 day ago by
Jacek
▴ 20
0
votes
0
replies
118
views
GO analysis custom reference?
GO-analysis
updated 1 day ago by
Ram
44k • written 1 day ago by
Pit
• 0
0
votes
2
replies
161
views
Query on WES
WES
1 day ago by
rauf.sania786
• 0
5
votes
15
replies
6.3k
views
9 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 1 day ago by
Mensur Dlakic
★ 29k • written 5 months ago by
Martina
• 0
0
votes
0
replies
105
views
News:
Introduction to Machine Learning in R online course
R
statistics
AI
machine-learning
updated 1 day ago by
Ram
44k • written 1 day ago by
Transmitting Science communication
▴ 70
6
votes
6
replies
382
views
Nanopore long-read sequencing doubts and problems
minmap2
long-reads
NanoPlot
Nanopore
updated 1 day ago by
lieven.sterck
15k • written 2 days ago by
ferran.llobet
▴ 10
0
votes
0
replies
105
views
Query Regarding Missing Sample Paths in Graph-Based Pangenome Construction
pangenome
variant_calling
giraffe
vg
haplotypes
1 day ago by
s_135
▴ 10
1
vote
3
replies
250
views
cannot install GO.db in windows
GO.db
updated 1 day ago by
i.sudbery
21k • written 2 days ago by
Naila
• 0
1
vote
5
replies
283
views
conda :FileNotFoundError: [Errno 2] No such file or directory
conda
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
JieQY
• 0
6
votes
5
replies
259
views
Samtools view only showing read2 for PE mapped reads
Samtools
mem2
bwa
flagstat
mapping
updated 2 days ago by
Pierre Lindenbaum
165k • written 2 days ago by
knickknack
• 0
0
votes
3
replies
264
views
Color AlphaFold PDB by B-Factor (pLDDT) in PyMol
pdb
pymol
updated 1 day ago by
Mensur Dlakic
★ 29k • written 3 days ago by
Schmoho
▴ 10
2
votes
2
replies
230
views
How to Resolve Overlapping Peaks in Sanger Chromatograms?
sequence-analysis
sanger-sequencing
dna-sequencing
chromatogram
2 days ago by
JOSÉ
• 0
4
votes
7
replies
327
views
Manual conversion of VCF genotypes to nucleotide sequence
vcf
nucleotide
sequence
updated 2 days ago by
Ram
44k • written 3 days ago by
endretoth
▴ 40
2
votes
3
replies
328
views
How to remove rows with empty gene symbols from a seurat object?
seurat
updated 3 days ago by
Michael
55k • written 5 days ago by
Chris
▴ 360
4
votes
11
replies
607
views
7 follow
Phylogenetic tree from whole genome using BUSCO
BUSCO
whole_genome
phylogenetic_tree
updated 3 days ago by
colindaven
7.2k • written 6 days ago by
manaswiniparija3
▴ 60
0
votes
0
replies
161
views
News:
Course on Ancient Metagenomics - online, 27-29 May
ancientDNA
Metagenomics
aMeta
3 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
670
views
Difference between trim galore report and Fastqc pre trimming
trim-galore
updated 2 days ago by
Ram
44k • written 2.6 years ago by
Luern
• 0
0
votes
0
replies
192
views
From Cram to gVCF
Cram
gVCF
4 days ago by
heureuse
• 0
2
votes
4
replies
1.4k
views
R CytoTRACE2 Results: Potency Score of Naive B Cells Lower Than Memory B and Plasmablasts – Contradicts Biological Knowledge
CytoTRACE2
3 days ago by
Binghong
▴ 20
3
votes
1
reply
351
views
Rules for Assigning Start and End Phase to Coding Exons
stare_phase
reading_frame
end_phase
updated 4 days ago by
Jorge - Ensembl
▴ 10 • written 7 days ago by
Milica
▴ 20
0
votes
1
reply
219
views
converting transcript positions to genomic locations
genomic
locations
updated 4 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
baibhu1234
▴ 20
120,529 results • Page
1 of 2411
Recent Votes
Mitochondrial Variant Calling Tools
Comment: Mitochondrial Variant Calling Tools
Sequence Length Distribution From A Fastq File
C: Sequence Length Distribution From A Fastq File
Comment: Training Augustus for Gene Prediction
Answer: Training Augustus for Gene Prediction
Answer: How does Salmon bootstrapping work?
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Recent Replies
Comment: cellxgene DNA Methylation data
by
LChart
4.9k
That may well be the raw beta values (n_cell x n_cpg)
Comment: How are probabilities of insertions and deletions encoded in FASTQ?
by
Jeremy Leipzig
23k
Yes they calibrate the base qualities called off the machine so that they add up to the real world empirical quality of your read, but ther…
Answer: NCBI genome submission validation error
by
lieven.sterck
15k
In general: if there are not too many issues: dig in manual and resolve them. Open the genome +annotation file in a genome browser/edito…
Comment: Training Augustus for Gene Prediction
by
Buffo
★ 2.4k
I've tested Braker2 using RNAseq on a non-model organism, and it does a terrible job. The main problem is the intron prediction.
Answer: Training Augustus for Gene Prediction
by
colindaven
7.2k
GALBA can help you to train Augustus models on your genome https://github.com/Gaius-Augustus/GALBA?tab=readme-ov-file#what-is-galba That…
Comment: cellxgene DNA Methylation data
by
1769mkc
★ 1.2k
I did try one of the single cell methylation data where I do find the size of the .mtx file is in this range 79G values.mtx So lo…
Answer: Mus musculus genome scaffold discrepancy
by
Wayne
★ 2.1k
See [How are genome assemblies generated and what are assembly levels?](https://support.nlm.nih.gov/kbArticle/?pn=KA-03568): The 305 conti…
Comment: Edit Dataset FASTQ files using ReadStore Command Line Interface
by
ATpoint
87k
This is commercial software, so usually we recommend to contact their support.
Answer: Fast querying of variant metrics with database
by
Pierre Lindenbaum
165k
> Are there any other alternative approaches I could take? binning data. Use a 'bin' column /index in your sql database. https://www.bios…
Comment: Mitochondrial Variant Calling Tools
by
Pierre Lindenbaum
165k
you already asked : https://www.biostars.org/p/9608685/
Comment: SpliceAI custom gene annotation file
by
ClkElf
▴ 50
Dear benformatics, Thank you very much for your comment. I tried that script previously, but the output is transcript-level, not gene-level…
Answer: How to use harmony with scanpy?
by
Rezin
• 0
You can explicitly use X_pca_harmony as below: sc.tl.umap(adata, init_pos='X_pca_harmony') sc.pl.umap(adata, ['Your_group']) Anyw…
Answer: SpliceAI custom gene annotation file
by
benformatics
4.1k
https://github.com/broadinstitute/SpliceAI-lookup/blob/master/annotations/convert_gtf_to_SpliceAI_annotation_input_format.py
Comment: RNA variant calling - SNP and indels files
by
Nerelys
• 0
Thank you for your reply. I will try this option :)
Comment: RNA variant calling - SNP and indels files
by
Nerelys
• 0
Thank you for your reply. It directly does not run the pipeline. I had to deactivate the module of GATK base calibration to run the pipeline
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