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116,918 results • Page
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59
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Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 52 minutes ago by
ATpoint
82k • written 7 hours ago by
Chen
• 0
0
votes
1
reply
47
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 51 minutes ago by
ATpoint
82k • written 4 hours ago by
Pegasus
▴ 100
0
votes
1
reply
38
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 55 minutes ago by
ATpoint
82k • written 4 hours ago by
Emily
▴ 20
0
votes
1
reply
66
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 32 minutes ago by
zx8754
11k • written 7 hours ago by
ohtang7
▴ 40
0
votes
0
replies
19
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
2 hours ago by
Spring
• 0
0
votes
1
reply
25
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
updated 59 minutes ago by
Pierre Lindenbaum
161k • written 2 hours ago by
IdaHao0921
• 0
0
votes
3
replies
228
views
Snakemake wrapper issue
fastqc
snakemake
1 hour ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
45
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
4 hours ago by
Holly
• 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
2.7k • written 7.4 years ago by
Istvan Albert
100k
2
votes
5
replies
154
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 4 hours ago by
Philipp Bayer
8.5k • written 8 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 5 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
0
replies
41
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
6 hours ago by
ntsopoul
▴ 60
0
votes
1
reply
77
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
7 hours ago by
Arton
• 0
0
votes
0
replies
45
views
Biomart issue, why so few 3'utrs?
utr
biomart
8 hours ago by
RNAseqer
▴ 270
0
votes
4
replies
104
views
Help with IGV abbreviation
Genome
browser
7 hours ago by
GeneC
• 0
0
votes
1
reply
96
views
How to process Bulk WES data?
WES
WGS
updated 10 hours ago by
GenoMax
142k • written 10 hours ago by
wyuan37
• 0
0
votes
1
reply
100
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 9 hours ago by
GenoMax
142k • written 11 hours ago by
cedric.blais
• 0
0
votes
2
replies
372
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
12 hours ago by
David Langenberger
11k
0
votes
1
reply
87
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 10 hours ago by
Ram
43k • written 12 hours ago by
eking28
• 0
1
vote
4
replies
351
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 12 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
312
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
13 hours ago by
kalavattam
▴ 190
0
votes
1
reply
143
views
How to interpret infinite odds ratio?
statistics
updated 13 hours ago by
bhumm
▴ 140 • written 18 hours ago by
Lukas
• 0
1
vote
2
replies
114
views
Duplicated sequence samtools
bowtie2
samtools
updated 14 hours ago by
GenoMax
142k • written 15 hours ago by
Moinuddin
• 0
0
votes
0
replies
59
views
reference-free assembly error assessment tools
assembly
15 hours ago by
lagartija
▴ 160
1
vote
2
replies
150
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 15 hours ago by
lagartija
▴ 160 • written 20 hours ago by
Esraa
• 0
1
vote
0
replies
62
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
15 hours ago by
J.
▴ 10
0
votes
0
replies
75
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
15 hours ago by
Biostar
2.7k
0
votes
1
reply
87
views
Splitting Seurat object by sample layers
seurat
updated 10 hours ago by
Ram
43k • written 16 hours ago by
kilcdincer
▴ 10
0
votes
3
replies
144
views
Galaxy StringTie error
stringtie
galaxy
updated 8 hours ago by
Mathew
▴ 130 • written 16 hours ago by
trkfs
• 0
0
votes
0
replies
63
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
18 hours ago by
atariw
▴ 10
0
votes
1
reply
109
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 18 hours ago by
GenoMax
142k • written 1 day ago by
octpus616
▴ 100
1
vote
3
replies
109
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
just now by
Vijith
▴ 30
0
votes
1
reply
111
views
consensus sequence calling
consensus
updated 16 hours ago by
bk11
★ 2.4k • written 20 hours ago by
Ghada
• 0
0
votes
3
replies
135
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 10 hours ago by
Ram
43k • written 20 hours ago by
yau
• 0
3
votes
2
replies
225
views
imputation through beagle
panel
beagle
reference
imputation
20 minutes ago by
analyst
▴ 50
0
votes
0
replies
61
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
20 hours ago by
JACKY
▴ 140
0
votes
1
reply
388
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 20 hours ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
1
vote
1
reply
174
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 21 hours ago by
aw7
▴ 280 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
73
views
Reference panel of normals for ensembl named refgenome
Mutect2
22 hours ago by
gernophil
▴ 80
1
vote
0
replies
71
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
22 hours ago by
tomas4482
▴ 400
2
votes
4
replies
222
views
BWA alignment
Samtools
bam
updated 50 minutes ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
3
votes
2
replies
143
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 22 hours ago by
ATpoint
82k • written 23 hours ago by
jennyp0706
• 0
0
votes
1
reply
133
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 23 hours ago by
Philipp Bayer
8.5k • written 1 day ago by
samRayne
• 0
0
votes
1
reply
218
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 10 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
2
votes
13
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
170
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
0
votes
0
replies
88
views
lncRNA
tcga
lncrna
1 day ago by
jain72744
▴ 10
0
votes
1
reply
214
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
jain72744
▴ 10
2
votes
5
replies
524
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
arctic
▴ 40 • written 10 days ago by
M.
▴ 30
1
vote
2
replies
312
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 16 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
116,918 results • Page
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Recent Votes
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
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Recent Replies
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…
Answer: The total expressed genes in RNA-Seq data
by
ATpoint
82k
There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
Answer: What is the bin size for Bamcompare?
by
ATpoint
82k
It is the number of adjacent bases that are aggregated (binned) into a single value. I find binning not optimal, and would always set this …
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
by
Pierre Lindenbaum
161k
see VQSR https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR and https://gatk.broadinst…
Comment: Snakemake wrapper issue
by
Matvii Mykhailichenko
• 0
Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you…
Answer: Is there any way to modify this pie chart ?
by
marco.barr
▴ 100
Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
Answer: Snakemake wrapper issue
by
Wei-Chen Pan
• 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results?
by
林明德
• 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
Answer: MGLTools does not work in windows 11
by
Ashfaq
• 0
In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
funny enough i tried the same thing (i've used BUSCO heaps times but never saw the E:! even the manual lists 'C:89.0%[S:85.8%,D:3.2%],F:6.9…
Comment: What does the 'E%' represent in BUSCO results?
by
GenoMax
142k
According to ChatGPT: In BUSCO, the "E" category represents "End" or "Endof" gene fragments. These are orthologous groups for which the ge…
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you for the link and details
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