Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
396 results • Page
4 of 8
Sort: replies
Rank
Views
Votes
Replies
1
vote
2
replies
274
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
11 days ago by
rianna.collins
• 0
0
votes
2
replies
314
views
bam merging for archaic samples
samtools
bam
updated 22 days ago by
Ram
43k • written 23 days ago by
Matteo Ungaro
▴ 100
0
votes
2
replies
312
views
How to update R on ubuntu
installation
update
R
apt-get
14 days ago by
Bosberg
▴ 50
0
votes
2
replies
461
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
24 days ago by
Ashok
• 0
2
votes
2
replies
643
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 27 days ago by
Ram
43k • written 2.7 years ago by
Yoonji
▴ 10
0
votes
2
replies
297
views
Bedmethyl file format
bedmethyl
methylation
updated 26 days ago by
GenoMax
142k • written 26 days ago by
njornet
▴ 20
0
votes
1
reply
199
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 19 days ago by
Sofia
• 0 • written 19 days ago by
mawigoj318
• 0
1
vote
1
reply
515
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
24 days ago by
renan.igor
• 0
0
votes
1
reply
197
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 20 days ago by
GenoMax
142k • written 20 days ago by
Srinka
▴ 20
0
votes
1
reply
227
views
Finding batch and outlayers
Pca
updated 14 days ago by
christopher medway
▴ 460 • written 15 days ago by
Tigran
• 0
0
votes
1
reply
249
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Sony
▴ 10
0
votes
1
reply
166
views
Provean help
variant
Provean
updated 11 days ago by
Mensur Dlakic
★ 27k • written 11 days ago by
Arun Sai Kumar
• 0
0
votes
1
reply
75
views
How to process Bulk WES data?
WES
WGS
updated 4 hours ago by
GenoMax
142k • written 4 hours ago by
wyuan37
• 0
0
votes
1
reply
180
views
Microbial Signal Transduction Database
MiST
updated 3 days ago by
zx8754
11k • written 3 days ago by
Shravani
• 0
0
votes
1
reply
696
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 12 days ago by
Ram
43k • written 13 days ago by
Dr Huma Naz
• 0
0
votes
1
reply
155
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 21 days ago by
ATpoint
82k • written 21 days ago by
enanoide
• 0
0
votes
1
reply
317
views
Could you please assist in identifying this cluster?
single-cell
updated 24 days ago by
Ram
43k • written 24 days ago by
carolofharvest
▴ 40
0
votes
1
reply
198
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 12 days ago by
i.sudbery
19k • written 13 days ago by
Edmond
• 0
1
vote
1
reply
260
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 18 days ago by
ATpoint
82k • written 18 days ago by
AaronJaime
• 0
1
vote
1
reply
666
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 27 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
0
votes
1
reply
181
views
unable to get feature count results
featureCounts
updated 13 days ago by
Ram
43k • written 13 days ago by
Ravita
• 0
1
vote
1
reply
208
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
28 days ago by
CTLong
▴ 110
1
vote
1
reply
150
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 11 days ago by
Ram
43k • written 11 days ago by
marco.barr
▴ 100
1
vote
1
reply
449
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 23 days ago by
Gordon Smyth
★ 7.1k • written 25 days ago by
Chris
▴ 280
0
votes
1
reply
279
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 28 days ago by
GenoMax
142k • written 28 days ago by
haiying.kong
▴ 360
0
votes
1
reply
176
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 3 days ago by
GenoMax
142k • written 3 days ago by
maria.soler
• 0
0
votes
1
reply
191
views
Differential Accessibility
DiffBind
updated 14 days ago by
Ram
43k • written 14 days ago by
Shloka
• 0
0
votes
1
reply
529
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 18 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
0
votes
1
reply
243
views
Subsetting and merging back Seurat Object brings different results
Seurat
11 days ago by
Bine
▴ 60
0
votes
1
reply
207
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 20 days ago by
bk11
★ 2.4k • written 20 days ago by
alphaflylizard
• 0
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 25 days ago by
Ram
43k • written 6.7 years ago by
boymin2020
▴ 80
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 26 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
1
vote
1
reply
206
views
Failed kmer content
kmer
illumina
ngs
updated 20 days ago by
Ram
43k • written 20 days ago by
Kasturi
• 0
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 26 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
1
vote
1
reply
167
views
student
epitranscriptomics
updated 6 days ago by
ATpoint
82k • written 6 days ago by
useriwa
• 0
0
votes
1
reply
296
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 24 days ago by
GenoMax
142k • written 24 days ago by
bioyas
▴ 10
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 26 days ago by
Ram
43k • written 6.8 years ago by
Dipro
• 0
0
votes
1
reply
65
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 3 hours ago by
GenoMax
142k • written 5 hours ago by
cedric.blais
• 0
0
votes
1
reply
149
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 5 days ago by
Bastien Hervé
5.3k • written 6 days ago by
sooni
▴ 20
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 26 days ago by
Ram
43k • written 6.1 years ago by
Jun
• 0
0
votes
1
reply
165
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 12 days ago by
Ram
43k • written 12 days ago by
ernestine.kubi
• 0
0
votes
1
reply
186
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 19 days ago by
Mensur Dlakic
★ 27k • written 20 days ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
220
views
Freyja plot error
Freyja
updated 26 days ago by
Ram
43k • written 26 days ago by
Adyasha
• 0
0
votes
1
reply
416
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 25 days ago by
Ram
43k • written 20 months ago by
Muhammad
• 0
0
votes
1
reply
72
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 4 hours ago by
Ram
43k • written 6 hours ago by
eking28
• 0
0
votes
1
reply
204
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 20 days ago by
bk11
★ 2.4k • written 20 days ago by
Susmita Mandal
▴ 110
0
votes
1
reply
208
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 3 days ago by
curious
▴ 750 • written 3 days ago by
SeoGyun
• 0
0
votes
1
reply
203
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Amr
▴ 160
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 26 days ago by
Ram
43k • written 6.3 years ago by
jjrin
▴ 40
0
votes
1
reply
291
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 6 days ago by
andres.firrincieli
3.6k • written 7 days ago by
Antonio
• 0
396 results • Page
4 of 8
Recent Votes
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
A: Filtering of VCF, INFO DP or FORMAT DP
What is the difference between GRCh37 and hs37? And hg19?
Recent Locations •
All
United States,
just now
INBIOSIS,
3 minutes ago
UCLA,
4 minutes ago
Whitefish, MT,
4 minutes ago
United States,
4 minutes ago
Japan,
4 minutes ago
Singapore,
6 minutes ago
Recent Awards •
All
Popular Question
to
RNAseqer
▴ 270
Scholar
to
kalavattam
▴ 190
Scholar
to
dthorbur
★ 2.0k
Commentator
to
Santosh Anand
5.7k
Popular Question
to
lagartija
▴ 160
Popular Question
to
bioinfo
▴ 150
Popular Question
to
Sara
▴ 30
Recent Replies
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.4k
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
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you very much for helping with the details.
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
thank you :)
Answer: Filtering based on alternate allelic balance
by
Arton
• 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation
by
GenoMax
142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
Answer: Help with IGV abbreviation
by
Mathew
▴ 130
Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
Comment: Kraken2 database
by
Mathew
▴ 130
I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
Comment: Galaxy StringTie error
by
Mathew
▴ 130
I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
Comment: Can diamond prepdb be used to make a taxonomically aware database?
by
GenoMax
142k
Should be possible: https://www.biostars.org/p/430366/ Are you using an older version of `diamond`? Latest versions of `diamond` can use N…
Comment: SNPEff database building error
by
Fungal genetics
• 0
Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!" The headers are correct and sam…
Comment: Extracting named fasta sequences according to list with Biopython
by
Rubayetul
• 0
the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
Comment: How to process Bulk WES data?
by
GenoMax
142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
Comment: Empty .best and .sing2 Files After Running Demuxlet
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Traffic: 1718 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6