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1,000 results • Page
1 of 20
Sort: Rank
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Votes
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0
votes
0
replies
18
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 28 minutes ago by
GenoMax
142k • written 1 hour ago by
Dude
• 0
0
votes
0
replies
17
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
1 hour ago by
brunofelicianodeomena
• 0
0
votes
1
reply
47
views
Alphaphold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 2 hours ago by
Mensur Dlakic
★ 27k • written 3 hours ago by
mbrav005
• 0
0
votes
0
replies
35
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
4 hours ago by
sansan_96
▴ 90
0
votes
1
reply
73
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
updated 4 hours ago by
Mensur Dlakic
★ 27k • written 5 hours ago by
MarcosCosta
• 0
2
votes
2
replies
119
views
Genome Visualization Tools
bacterial
genome
updated 6 hours ago by
GenoMax
142k • written 6 hours ago by
dlera.lozano
▴ 10
1
vote
3
replies
131
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 5 hours ago by
Ram
43k • written 7 hours ago by
Prawesh
• 0
0
votes
1
reply
102
views
Using ggplotly in R
ggplot
ggplotly
updated 7 hours ago by
jared.andrews07
★ 16k • written 7 hours ago by
jen
▴ 10
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
1
reply
101
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 7 hours ago by
GenoMax
142k • written 8 hours ago by
bioinfo
▴ 150
0
votes
3
replies
184
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 8 hours ago by
noodle
▴ 580 • written 12 hours ago by
doramora
▴ 10
0
votes
1
reply
90
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 9 hours ago by
LauferVA
4.2k • written 10 hours ago by
graeme.thorn
▴ 100
0
votes
1
reply
89
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 9 hours ago by
GenoMax
142k • written 10 hours ago by
melissa.joubert
• 0
0
votes
0
replies
67
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
10 hours ago by
ramiro.barrantes
• 0
4
votes
1
reply
156
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
12 hours ago by
J.
▴ 40
0
votes
0
replies
65
views
Is there a real ground truth for CNV data?
CNV
13 hours ago by
jennyp0706
• 0
0
votes
3
replies
164
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 13 hours ago by
GenoMax
142k • written 1 day ago by
RNAseqer
▴ 270
1
vote
1
reply
101
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 8 hours ago by
Ram
43k • written 13 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
58
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 14 hours ago by
GenoMax
142k • written 14 hours ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 16 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
6
replies
282
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
10 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
161
views
How to access GWAVA software of data
GWAVA
updated 14 hours ago by
GenoMax
142k • written 17 hours ago by
nonaddldy
▴ 10
0
votes
1
reply
131
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 19 hours ago by
ATpoint
82k • written 1 day ago by
Chen
• 0
1
vote
1
reply
129
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 18 hours ago by
ATpoint
82k • written 23 hours ago by
Pegasus
▴ 100
0
votes
1
reply
103
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 5 hours ago by
Ram
43k • written 23 hours ago by
Emily
▴ 20
1
vote
1
reply
148
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 19 hours ago by
zx8754
11k • written 1 day ago by
ohtang7
▴ 40
0
votes
0
replies
68
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
21 hours ago by
Spring
• 0
0
votes
2
replies
140
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
18 hours ago by
IdaHao0921
• 0
0
votes
3
replies
308
views
Snakemake wrapper issue
fastqc
snakemake
updated 22 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
91
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
23 hours ago by
Holly
• 0
2
votes
5
replies
223
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 23 hours 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 5 hours ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
1
reply
113
views
Filtering based on alternate allelic balance
GATK
VCF
updated 5 hours ago by
Ram
43k • written 1 day ago by
Arton
• 0
2
votes
4
replies
176
views
Help with IGV abbreviation
igv
updated 5 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
0
votes
1
reply
134
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
135
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
399
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
123
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
437
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 5 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
3
replies
364
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
238
views
How to interpret infinite odds ratio?
statistics
16 hours ago by
Lukas
• 0
1
vote
2
replies
149
views
Duplicated sequence samtools
bowtie2
samtools
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Moinuddin
• 0
0
votes
0
replies
89
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
1
vote
2
replies
187
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
123
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
1 day ago by
Biostar
2.8k
0
votes
1
reply
121
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
221
views
Galaxy StringTie error
stringtie
galaxy
16 hours ago by
trkfs
• 0
0
votes
0
replies
88
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
1 day ago by
atariw
▴ 10
0
votes
1
reply
138
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 1 day ago by
GenoMax
142k • written 2 days ago by
octpus616
▴ 100
1
vote
4
replies
249
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 1 hour ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
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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
Genome Visualization Tools
Answer: Genome Visualization Tools
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
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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/…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
GenoMax
142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content
by
noodle
▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
by
wyuan37
• 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file?
by
wyuan37
• 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses
by
LauferVA
4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
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