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
500 results • Page
5 of 10
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
276
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
16 days ago by
ramin.k2013
• 0
0
votes
0
replies
163
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 18 days ago by
Ram
43k • written 18 days ago by
ramin.k2013
• 0
0
votes
1
reply
177
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 18 days ago by
Pierre Lindenbaum
161k • written 18 days ago by
sainavyav22
• 0
0
votes
9
replies
598
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 17 days ago by
LauferVA
4.2k • written 18 days ago by
Aki
▴ 20
0
votes
0
replies
99
views
Issue while using circle_dat function from GOplot in R
GOplot
R
18 days ago by
ckelly96
• 0
0
votes
2
replies
202
views
Can't figure out plink --sample-diff
plink
19 days ago by
curious
▴ 750
0
votes
1
reply
154
views
Geneious Prime (Consense Sequence)
Consense
Sequence
updated 19 days ago by
GenoMax
141k • written 19 days ago by
Reno
• 0
1
vote
2
replies
226
views
convert a seurat object to expressionset
Seurat
18 days ago by
Bine
▴ 60
2
votes
4
replies
405
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 19 days ago by
GenoMax
141k • written 20 days ago by
pl.terzian
• 0
0
votes
0
replies
123
views
Inferring cell identity/genotype in single cells with missing information
cell
seurat
single
score
19 days ago by
txema.heredia
▴ 110
0
votes
0
replies
105
views
cibersortx colnames
gema122
19 days ago by
gem1
• 0
0
votes
2
replies
226
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
17 days ago by
marongiu.luigi
▴ 710
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 19 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
0
replies
105
views
Confused about the results of a function in dada2 pipeline sample inference step
Microbiome
R
dada2
19 days ago by
Mohamed Samir
▴ 20
1
vote
4
replies
820
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
19 days ago by
Hyper_Odin
▴ 310
2
votes
4
replies
301
views
Addmetadata to seurat obj
seurat
18 days ago by
synat.keam
▴ 100
0
votes
0
replies
103
views
Methylation array analysis using dmpFinder
epic
methylation
normalization
dmp
mset
19 days ago by
Roy
▴ 10
0
votes
0
replies
193
views
Confused by the `--ld-window` flag in Vcftools. What does the number of SNPs between SNPs mean?
tabix
vcftools
19 days ago by
rijan_dhakal2055
• 0
0
votes
5
replies
406
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 19 days ago by
GenoMax
141k • written 19 days ago by
Shay
• 0
0
votes
0
replies
108
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
19 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
253
views
Problem with downloading genome in SnpEff
SnpEff
19 days ago by
Javier
• 0
0
votes
0
replies
110
views
Comparison between Bracken outputs
Bracken
Kraken
Taxonomy
20 days ago by
SushiRoll
▴ 120
0
votes
4
replies
281
views
Adaptive sampling for whole chromosomes
T2T
Nanopore
AdaptiveSampling
aneuploidy
centromeres
19 days ago by
njornet
▴ 20
0
votes
0
replies
124
views
DESeq2 LRT divergent DEGs ?
interaction
LRT
deseq2
20 days ago by
klervi-lugue
• 0
0
votes
2
replies
225
views
BLASTP short sequences (<20aa) - interpreting results
blast
sequence
blastp
alignment
19 days ago by
neish
• 0
0
votes
3
replies
271
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 19 days ago by
noodle
▴ 570 • written 20 days ago by
CrisRisu
• 0
0
votes
1
reply
171
views
P-values for pairwise FST
FST
P-value
pairwise
updated 20 days ago by
dthorbur
★ 1.9k • written 20 days ago by
Emy
▴ 50
0
votes
4
replies
343
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 18 days ago by
GenoMax
141k • written 20 days ago by
Soohyun
• 0
0
votes
0
replies
260
views
batch correction: cds from seurat
batch-correction
R
seurat
monocle3
cds
updated 20 days ago by
Ram
43k • written 20 days ago by
sooni
▴ 20
0
votes
0
replies
143
views
Seurat Package
seurat
20 days ago by
odi
▴ 10
0
votes
0
replies
124
views
RUVg correction
differential-expression
ruvseq
updated 19 days ago by
Ram
43k • written 20 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
129
views
How to annotate pairwise p value from limma (3 groups) in a combine multiple boxplot?
limma
boxplot
19 days ago by
Chris
▴ 260
0
votes
0
replies
135
views
Methylation workflow problem
rstudio
methylation
updated 20 days ago by
Ram
43k • written 20 days ago by
Roy
▴ 10
0
votes
0
replies
133
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
20 days ago by
Thomas
• 0
2
votes
2
replies
268
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
13 days ago by
bioinfo
▴ 150
0
votes
5
replies
549
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 20 days ago by
Ram
43k • written 24 days ago by
Greg
• 0
0
votes
1
reply
209
views
Pattern of GC content across reads from fastp
multiqc
ddRAD
updated 20 days ago by
GenoMax
141k • written 20 days ago by
jberg
• 0
2
votes
6
replies
413
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
20 days ago by
jkim
▴ 170
0
votes
0
replies
116
views
RNA velocity after SoupX in single cell data
soupX
scrna
transcriptomics
nuclei
updated 20 days ago by
GenoMax
141k • written 20 days ago by
shersky
• 0
0
votes
0
replies
114
views
What is more important for Structural Variant Calling? Recall or Precision?
structural-variants
merging
precision-recall
21 days ago by
Luke
• 0
1
vote
1
reply
466
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 20 days ago by
chrchang523
10k • written 21 days ago by
dsbusiness135
▴ 10
1
vote
2
replies
209
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
20 days ago by
phhelou5
• 0
0
votes
1
reply
267
views
How to do further funtional analysis of DEG KeggGet output list?
KEGGREST
DESEQ2
RNA-Seq
DEG
21 days ago by
joana.maclean
• 0
8
votes
10
replies
720
views
bash script
whole-genome-sequencing
updated 13 days ago by
Ram
43k • written 21 days ago by
bestone
▴ 30
0
votes
0
replies
123
views
Confusion with somatic variant calling: Advice on Ensembl-compatible resources?
GATK
Mutect2
ensembl
20 days ago by
DGTool
• 0
1
vote
2
replies
243
views
permutation test in edgeR
rna-seq
edgeR
updated 7 days ago by
Gordon Smyth
★ 7.0k • written 21 days ago by
Netanel
• 0
0
votes
0
replies
277
views
Different rsID for the same chromsome, position, ref & alt allele depending on different data sources. Which one should I use?
UKB
rsID
UKB-PPP
ensembl-vep
dbsnp
19 days ago by
lsy9
▴ 20
0
votes
0
replies
136
views
How can I plot the PCA with the raw count mRNA seq data?
PCA
normalization
updated 20 days ago by
Ram
43k • written 21 days ago by
Yoomi
▴ 20
0
votes
0
replies
117
views
Blast2GO Fisher test
Fisher-test
Go-annotation
Blast2GO
updated 20 days ago by
Ram
43k • written 21 days ago by
BlackM
• 0
0
votes
1
reply
167
views
How do I run fastq-dump on multiple prefetched files at once?
sratoolkit
fastq-dump
updated 21 days ago by
Pierre Lindenbaum
161k • written 21 days ago by
biotrekker
▴ 100
500 results • Page
5 of 10
Recent Votes
Answer: what is the purpose of indexing the reference genome (Kallisto)
The Biostar Herald for Monday, April 29, 2024
The Biostar Herald for Monday, April 29, 2024
Comment: NGS forensics: how to know if data is fabricated
Answer: High Malat-1 expression in single cell data
Answer: High Malat-1 expression in single cell data
The Biostar Herald for Monday, April 29, 2024
Recent Locations •
All
United States,
just now
United States,
just now
Sheffield, UK,
1 minute ago
France,
2 minutes ago
United Kingdom,
3 minutes ago
Germany,
3 minutes ago
UCLA,
3 minutes ago
Recent Awards •
All
Popular Question
to
Bine
▴ 60
Popular Question
to
Deepak Tanwar
★ 4.2k
Popular Question
to
Chris
▴ 260
Popular Question
to
Trivas
★ 1.7k
Popular Question
to
noodle
▴ 570
Popular Question
to
SaltedPork
▴ 170
Popular Question
to
christopher medway
▴ 450
Recent Replies
Comment: Genbank File Format
by
GenoMax
141k
Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this in…
Comment: Downsampling fastq file
by
Ram
43k
The file being PE should not matter. I'd recommend you open an issue on the seqtk github repo as this is starting to look like some sort of…
Comment: CWl and toil singularity image e.g busybox? Thank you
by
Ram
43k
Do the developers of toil mention biostars? Where do they direct their support requests to?
Comment: How should I make kallisto indexes?
by
dsull
★ 5.9k
As an additional note, all those ``--include-attribute`` stuff was basically to restrict the transcriptome to precisely the items that Cell…
Answer: How should I make kallisto indexes?
by
dsull
★ 5.9k
I recommend the ``kb ref`` method for two reasons: 1. The index created will yield more accurate mapping for datasets that have a substa…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
Were these samples barcoded when they were run. If not then you won't be able to do much.
Comment: ScRNA data question
by
bk11
★ 2.4k
The approach you are using here is the old method. Seurat is updated to V5. Please try Seurat V5 integrative analysis described in the link…
Answer: How should I make kallisto indexes?
by
Bajaj
• 0
Hi, you can still use `kallisto index -i transcripts.index transcripts.fa` (extract the gz file) for making index files. I have tried it an…
Comment: How to update R on ubuntu
by
Bosberg
▴ 50
Thanks for the suggestion, but I get several lines of results (see below) and although there are directories called `"R"`, I can't find any…
Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
Malat1 is a lncRNA abundant in the nucleus. I guess if Malat1 is abundant and stable, makes sense it could be detect in high amounts in scR…
Comment: CWl and toil singularity image e.g busybox? Thank you
by
Fadi
• 0
Where can I ask this question? Apparently this the place where you can help for toil?
Comment: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Dear Gordon, excuse me for not being specific regarding your advice. What would be the best way if I wanted to add new annotations to the …
Comment: Programmatically retrieving positions of protein active site residues
by
GenoMax
141k
While you wait to get answers, consider asking ChatGPT for a solution. You may be pleasantly surprised with pointers/code you will get.
Comment: High Malat-1 expression in single cell data
by
Kazo
▴ 10
When I perform differential analysis, the genes that could be considered as markers in this malat1 high cluster tend to be nuclear genes. D…
Comment: How to update R on ubuntu
by
GenoMax
141k
You can check where the application was installed using: https://unix.stackexchange.com/questions/39590/apt-get-install-where-does-it-go T…
Traffic: 3180 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