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116,921 results • Page
1 of 2339
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sci-RNA-seq
sci-RNA-seq
clusters
combinatorial
single
just now by
kilcdincer
▴ 10
0
votes
0
replies
9
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 11 minutes ago by
GenoMax
142k • written 25 minutes ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 2 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
2
replies
107
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 2 hours ago by
ATpoint
82k • written 12 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
70
views
How to access GWAVA software of data
GWAVA
updated 43 minutes ago by
GenoMax
142k • written 3 hours ago by
nonaddldy
▴ 10
0
votes
1
reply
96
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 6 hours ago by
ATpoint
82k • written 12 hours ago by
Chen
• 0
0
votes
1
reply
84
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 4 hours ago by
ATpoint
82k • written 9 hours ago by
Pegasus
▴ 100
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
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
74
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 6 hours ago by
ATpoint
82k • written 9 hours ago by
Emily
▴ 20
1
vote
1
reply
108
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 5 hours ago by
zx8754
11k • written 12 hours ago by
ohtang7
▴ 40
0
votes
0
replies
44
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
7 hours ago by
Spring
• 0
0
votes
2
replies
99
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
4 hours ago by
IdaHao0921
• 0
0
votes
3
replies
272
views
Snakemake wrapper issue
fastqc
snakemake
updated 8 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
59
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
9 hours ago by
Holly
• 0
2
votes
5
replies
188
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 9 hours ago by
Philipp Bayer
8.5k • written 13 hours ago by
林明德
• 0
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 10 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
1
reply
90
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
13 hours ago by
Arton
• 0
0
votes
0
replies
56
views
Biomart issue, why so few 3'utrs?
utr
biomart
13 hours ago by
RNAseqer
▴ 270
1
vote
4
replies
131
views
Help with IGV abbreviation
Genome
browser
12 hours ago by
GeneC
• 0
0
votes
1
reply
111
views
How to process Bulk WES data?
WES
WGS
updated 15 hours ago by
GenoMax
142k • written 16 hours ago by
wyuan37
• 0
0
votes
1
reply
111
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 14 hours ago by
GenoMax
142k • written 16 hours ago by
cedric.blais
• 0
0
votes
2
replies
382
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
17 hours ago by
David Langenberger
11k
0
votes
1
reply
95
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 15 hours ago by
Ram
43k • written 17 hours ago by
eking28
• 0
1
vote
4
replies
362
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 17 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
322
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
18 hours ago by
kalavattam
▴ 190
1
vote
2
replies
188
views
How to interpret infinite odds ratio?
statistics
3 hours ago by
Lukas
• 0
1
vote
2
replies
124
views
Duplicated sequence samtools
bowtie2
samtools
updated 19 hours ago by
GenoMax
142k • written 20 hours ago by
Moinuddin
• 0
0
votes
0
replies
68
views
reference-free assembly error assessment tools
assembly
20 hours ago by
lagartija
▴ 160
1
vote
2
replies
161
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 20 hours ago by
lagartija
▴ 160 • written 1 day ago by
Esraa
• 0
1
vote
0
replies
70
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
21 hours ago by
J.
▴ 10
0
votes
0
replies
88
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
21 hours ago by
Biostar
2.7k
0
votes
1
reply
99
views
Splitting Seurat object by sample layers
seurat
updated 15 hours ago by
Ram
43k • written 21 hours ago by
kilcdincer
▴ 10
0
votes
4
replies
178
views
Galaxy StringTie error
stringtie
galaxy
2 hours ago by
trkfs
• 0
0
votes
0
replies
71
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
23 hours ago by
atariw
▴ 10
0
votes
1
reply
119
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 1 day ago by
GenoMax
142k • written 1 day ago by
octpus616
▴ 100
1
vote
3
replies
191
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
5 hours ago by
Vijith
▴ 30
0
votes
1
reply
120
views
consensus sequence calling
consensus
updated 21 hours ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
3
replies
144
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 15 hours ago by
Ram
43k • written 1 day ago by
yau
• 0
3
votes
2
replies
235
views
imputation through beagle
panel
beagle
reference
imputation
5 hours ago by
analyst
▴ 50
0
votes
0
replies
69
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
1 day ago by
JACKY
▴ 140
0
votes
1
reply
432
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 1 day ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
1
vote
1
reply
184
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 1 day ago by
aw7
▴ 280 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
83
views
Reference panel of normals for ensembl named refgenome
Mutect2
1 day ago by
gernophil
▴ 80
1
vote
0
replies
80
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
1 day ago by
tomas4482
▴ 400
2
votes
4
replies
257
views
BWA alignment
Samtools
bam
updated 6 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
3
votes
2
replies
158
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 1 day ago by
ATpoint
82k • written 1 day ago by
jennyp0706
• 0
0
votes
1
reply
142
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 1 day ago by
Philipp Bayer
8.5k • written 1 day ago by
samRayne
• 0
0
votes
1
reply
225
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 15 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
178
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 1 day ago by
chrchang523
10k • written 6 days ago by
analyst
▴ 50
116,921 results • Page
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Comment: Help with IGV abbreviation
A: How to get read counts on transcript level using featurecounts?
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Answer: How to interpret infinite odds ratio?
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Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
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Recent Replies
Comment: How to access GWAVA software of data
by
GenoMax
142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: Overlapping Ranges within Granges object
by
ATpoint
82k
There is no one-hit function in GenomicRanges, but you can stick something together using a combination of `findOverlaps` to first find ove…
Comment: Galaxy StringTie error
by
trkfs
• 0
Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank…
Comment: How to interpret infinite odds ratio?
by
Lukas
• 0
Thanks you for your answer. But according that links interpretation of inf odds ratio is up to hypothesis of the researcher.So my solution …
Comment: How to access GWAVA software of data
by
nonaddldy
▴ 10
Not found in https://ftp.sanger.ac.uk/resources/software/gwava/ ![][1] [1]: /media/images/f69695ec-e047-44f6-95ce-cd4edf1c
Comment: How to access GWAVA software of data
by
nonaddldy
▴ 10
https://www.sanger.ac.uk/tool/gwava/
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
by
IdaHao0921
• 0
The species I study is not a model species, VQSR can not be applied here. I already used gatk hard-filtering. I mean, after hard-filtering,…
Answer: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment
by
ATpoint
82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation
by
ATpoint
82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
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