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116,934 results • Page
1 of 2339
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12
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
58 minutes ago by
Arton
• 0
0
votes
0
replies
13
views
Forum:
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
1 hour ago by
iqra
• 0
0
votes
0
replies
32
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
Dude
• 0
795
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
0
replies
32
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
4 hours ago by
brunofelicianodeomena
• 0
0
votes
2
replies
73
views
Alphaphold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
1 hour ago by
mbrav005
• 0
0
votes
1
reply
55
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
1 hour ago by
sansan_96
▴ 90
0
votes
1
reply
80
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
updated 7 hours ago by
Mensur Dlakic
★ 27k • written 8 hours ago by
MarcosCosta
• 0
2
votes
2
replies
132
views
Genome Visualization Tools
bacterial
genome
updated 9 hours ago by
GenoMax
142k • written 9 hours ago by
dlera.lozano
▴ 10
1
vote
3
replies
142
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 8 hours ago by
Ram
43k • written 9 hours ago by
Prawesh
• 0
0
votes
2
replies
138
views
Using ggplotly in R
ggplot
ggplotly
2 hours ago by
jen
▴ 10
0
votes
1
reply
112
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 10 hours ago by
GenoMax
142k • written 11 hours ago by
bioinfo
▴ 150
0
votes
3
replies
197
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 11 hours ago by
noodle
▴ 580 • written 15 hours ago by
doramora
▴ 10
0
votes
1
reply
98
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 11 hours ago by
LauferVA
4.2k • written 12 hours ago by
graeme.thorn
▴ 100
0
votes
1
reply
96
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 12 hours ago by
GenoMax
142k • written 13 hours ago by
melissa.joubert
• 0
0
votes
0
replies
70
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
13 hours ago by
ramiro.barrantes
• 0
4
votes
1
reply
160
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
15 hours ago by
J.
▴ 40
0
votes
0
replies
69
views
Is there a real ground truth for CNV data?
CNV
15 hours ago by
jennyp0706
• 0
0
votes
3
replies
167
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 15 hours ago by
GenoMax
142k • written 1 day ago by
RNAseqer
▴ 270
1
vote
1
reply
103
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 11 hours ago by
Ram
43k • written 16 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
62
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 16 hours ago by
GenoMax
142k • written 16 hours ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 18 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
7
replies
298
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
1 hour ago by
ntsopoul
▴ 60
0
votes
3
replies
164
views
How to access GWAVA software of data
GWAVA
updated 17 hours ago by
GenoMax
142k • written 19 hours ago by
nonaddldy
▴ 10
0
votes
1
reply
136
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 22 hours ago by
ATpoint
82k • written 1 day ago by
Chen
• 0
1
vote
1
reply
135
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 21 hours ago by
ATpoint
82k • written 1 day ago by
Pegasus
▴ 100
0
votes
1
reply
105
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 8 hours ago by
Ram
43k • written 1 day ago by
Emily
▴ 20
1
vote
1
reply
152
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 22 hours ago by
zx8754
11k • written 1 day ago by
ohtang7
▴ 40
0
votes
0
replies
71
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
23 hours ago by
Spring
• 0
0
votes
2
replies
142
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
20 hours ago by
IdaHao0921
• 0
0
votes
3
replies
311
views
Snakemake wrapper issue
fastqc
snakemake
updated 1 day ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
94
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
1 day ago by
Holly
• 0
2
votes
5
replies
227
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 1 day ago by
Philipp Bayer
8.5k • written 1 day ago by
林明德
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 8 hours ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
180
views
Help with IGV abbreviation
igv
updated 8 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
0
votes
1
reply
138
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
1
reply
138
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 day ago by
GenoMax
142k • written 1 day ago by
cedric.blais
• 0
0
votes
2
replies
405
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
1 day ago by
David Langenberger
11k
0
votes
1
reply
127
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 1 day ago by
Ram
43k • written 1 day ago by
eking28
• 0
1
vote
5
replies
444
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 8 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
3
replies
380
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
1 day ago by
kalavattam
▴ 190
1
vote
2
replies
242
views
How to interpret infinite odds ratio?
statistics
19 hours ago by
Lukas
• 0
1
vote
2
replies
152
views
Duplicated sequence samtools
bowtie2
samtools
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Moinuddin
• 0
0
votes
0
replies
91
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
1
vote
2
replies
190
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 1 day ago by
lagartija
▴ 160 • written 1 day ago by
Esraa
• 0
2
votes
0
replies
126
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
1 day ago by
Biostar
2.8k
0
votes
1
reply
124
views
Splitting Seurat object by sample layers
seurat
updated 1 day ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
4
replies
226
views
Galaxy StringTie error
stringtie
galaxy
19 hours ago by
trkfs
• 0
0
votes
0
replies
92
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
1 day ago by
atariw
▴ 10
0
votes
1
reply
141
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 1 day ago by
GenoMax
142k • written 2 days ago by
octpus616
▴ 100
116,934 results • Page
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Recent Votes
Comment: How to calculate coverage of Nanopore long read data?
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
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Recent Replies
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
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