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120,527 results • Page
1 of 2411
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0
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8
views
Minimal Quality Control Thresholds in Shotgun or Amplicon Metagenomics for non assembly based analysis
QC
Microbiome
fastp
36 minutes ago by
Maxwell
▴ 50
0
votes
1
reply
22
views
NCBI genome submission validation error
genome
annotation
updated 45 minutes ago by
lieven.sterck
15k • written 55 minutes ago by
slin023
• 0
0
votes
0
replies
12
views
Estimating the Relative Abundance of a Species in a Mixed Microbial Community Using 16S PCR
16S
1 hour ago by
ljrdain2508
• 0
2
votes
2
replies
70
views
Training Augustus for Gene Prediction
Augustus
Busco
genome
prediction
gene
updated 1 hour ago by
Buffo
★ 2.4k • written 3 hours ago by
shiv
▴ 10
0
votes
1
reply
79
views
Mus musculus genome scaffold discrepancy
genome
ncbi
updated 4 hours ago by
Wayne
★ 2.1k • written 7 hours ago by
SJP
• 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
0
votes
1
reply
57
views
Edit Dataset FASTQ files using ReadStore Command Line Interface
FASTQ
Readstore
CLI
updated 6 hours ago by
ATpoint
87k • written 6 hours ago by
DNAStar
• 0
0
votes
0
replies
40
views
plyranges – joining gpos object only by the start coordinate of the range
GenomicRanges
plyranges
updated 6 hours ago by
Pierre Lindenbaum
165k • written 6 hours ago by
Kateřina
• 0
0
votes
1
reply
68
views
Fast querying of variant metrics with database
python
database
updated 7 hours ago by
Pierre Lindenbaum
165k • written 7 hours ago by
DBScan
▴ 470
2
votes
1
reply
77
views
Mitochondrial Variant Calling Tools
Mitochondrial
NGS
Variant
Calling
Illumina
updated 7 hours ago by
Pierre Lindenbaum
165k • written 8 hours ago by
adarsh_munna
▴ 60
1
vote
3
replies
458
views
How to use harmony with scanpy?
scanpy
harmony
updated 8 hours ago by
Rezin
• 0 • written 14 days ago by
bioinfo
▴ 150
1
vote
2
replies
89
views
SpliceAI custom gene annotation file
GENCODE
SpliceAI
6 hours ago by
ClkElf
▴ 50
0
votes
0
replies
59
views
Job:
Postdoc in Reproductive genetics - bioinformatics
Sweden
bioinformatics
genetics
postdoc
9 hours ago by
pol.sole.navais
• 0
0
votes
0
replies
78
views
What is a recommended maximum read depth threshold for DNA variant filtration, supported by scientific articles?
filtering
articles-search
read-depth
variant-calling
10 hours ago by
Sofya
• 0
9
votes
13
replies
2.3k
views
How are probabilities of insertions and deletions encoded in FASTQ?
fastq
phred quality score
nanopore
pacbio
indels
updated just now by
Jeremy Leipzig
23k • written 6.0 years ago by
shelkmike
★ 1.5k
0
votes
2
replies
108
views
samtools mpileup and samtools tview give different reads quality results
samtools
tview
mpileup
12 hours ago by
cocoboxt
• 0
9
votes
12
replies
7.2k
views
picard installation failure
error
software
picard
updated 13 hours ago by
lieven.sterck
15k • written 7.5 years ago by
sanariyaz21
• 0
0
votes
1
reply
108
views
low alignment rate for RNA-Seq data
rice
low
alignment
RNA-Seq
updated 14 hours ago by
michael.ante
★ 4.0k • written 16 hours ago by
analyst
▴ 60
2
votes
1
reply
107
views
Optimal Computer Configuration for Bioinformatics Analysis
scRNA-seq
computer
updated 13 hours ago by
ATpoint
87k • written 17 hours ago by
Song
▴ 10
0
votes
1
reply
127
views
Variant Missing in VCF but Present in BAM Files: Discrepancy Identified via IGV Report in Join-Call Project
GATK
Deepvariant
BWA
updated 16 hours ago by
Pierre Lindenbaum
165k • written 20 hours ago by
lunping98
• 0
0
votes
0
replies
71
views
no "-" strand in transcriptome alignment
DRS
transcriptome
alignment
7 hours ago by
baibhu1234
▴ 20
0
votes
0
replies
68
views
Anndata vs cloupe
seurat
cloupe
scanpy
anndata
22 hours ago by
Rika
• 0
0
votes
3
replies
155
views
Gene Mapping Issue
DAVID
updated 13 hours ago by
lieven.sterck
15k • written 23 hours ago by
won
• 0
0
votes
0
replies
92
views
Job:
Assistant, Associate, or Full Project Scientist in Molecular Biology
molecular
teaching
biology
1 day ago by
UCSDBioSci
▴ 30
2
votes
4
replies
200
views
RNA variant calling - SNP and indels files
mouse
variant_calling
genomics
RNA
9 hours ago by
Nerelys
• 0
2
votes
4
replies
184
views
Manta analysis in WES
Deletion
MANTA
WES
SV
Exomiser
1 day ago by
Eduardo
• 0
0
votes
1
reply
105
views
All VS All contamination check for tumor samples
tumor
contamination
15 hours ago by
mps
• 0
1
vote
2
replies
145
views
Determine binding sites in unstimulated TF ChIP-seq samples
ChIP-seq
csaw
1 day ago by
Jacek
▴ 20
0
votes
0
replies
113
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
157
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 21 hours ago by
Mensur Dlakic
★ 29k • written 5 months ago by
Martina
• 0
0
votes
0
replies
100
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
377
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
100
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
243
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
274
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
255
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
257
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
225
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
320
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
323
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
604
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
158
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
665
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
189
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
347
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
214
views
converting transcript positions to genomic locations
genomic
locations
updated 4 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
baibhu1234
▴ 20
0
votes
1
reply
249
views
Read groups RNA-seq and hisat2
hisat2
RNA-seq
read-groups
updated 4 days ago by
Ram
44k • written 4 days ago by
frarodmar17
• 0
0
votes
0
replies
186
views
simulate a genome with specific event
simulation
genome
retrocopy
4 days ago by
Matteo Ungaro
▴ 110
120,527 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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France/Nantes/Institut du Thorax - INSERM UMR1087,
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Popular Question
to
slin023
• 0
Popular Question
to
shiv
▴ 10
Popular Question
to
deepue
▴ 160
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to
predeus
★ 2.1k
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Biomonika (Noolean)
3.2k
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Manuel
▴ 50
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zizigolu
★ 4.3k
Recent Replies
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
Comment: samtools mpileup and samtools tview give different reads quality results
by
cocoboxt
• 0
Sry!!!I've uploaded a picture to make sure it's visible!!
Answer: How are probabilities of insertions and deletions encoded in FASTQ?
by
shelkmike
★ 1.5k
Answering my own question.<br> 1) The Phred quality scores of Oxford Nanopore reads take into account the probabilities of indel errors (h…
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