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 week
all time
today
this week
this month
this year
129 results • Page
3 of 3
Sort: replies
Rank
Views
Votes
Replies
0
votes
0
replies
68
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
1 day ago by
alifafiq1
• 0
0
votes
0
replies
76
views
Merging replicates from Encode project
CHIP-seq
encode
23 hours ago by
Nurken
• 0
0
votes
0
replies
24
views
Network Alignment
plugin
Cytoscape
CytoMCS
3 hours ago by
Akash D
▴ 40
0
votes
0
replies
67
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 20 hours ago by
Ram
43k • written 23 hours ago by
SHREYA
• 0
0
votes
0
replies
21
views
Alternative splicing
single-cell
suppa
rnaseq
splicing
alternative
2 hours ago by
newuser2024
• 0
0
votes
0
replies
89
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 20 hours ago by
Ram
43k • written 1 day ago by
Amélie
• 0
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 6 days ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
0
replies
62
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
19 hours ago by
ohtang7
▴ 40
0
votes
0
replies
76
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 19 hours ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
0
replies
26
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 hour ago by
Sergio
• 0
0
votes
0
replies
162
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 6 days ago by
GenoMax
141k • written 6 days ago by
srimmer
• 0
0
votes
0
replies
28
views
different FeatureCounts output for the same data
fpkm
rnaseq
Counts
Rsubread
updated just now by
GenoMax
141k • written 2 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
53
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
12 hours ago by
Kash
▴ 110
0
votes
0
replies
155
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 5 days ago by
Ram
43k • written 6 days ago by
bioinfo223
▴ 10
0
votes
0
replies
171
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
6 days ago by
P.
• 0
0
votes
0
replies
198
views
Lncipedia GTF file error
Proteomics
updated 4 days ago by
Ram
43k • written 5 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
200
views
Copy number variation plot
Copy-number-variation
genomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Emmi
• 0
0
votes
0
replies
163
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
6 days ago by
ekirsch
• 0
0
votes
0
replies
178
views
Chemical structure validation
structure
cap
validation
metabolite
4 days ago by
Rodolfo Adrián
• 0
0
votes
0
replies
5
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
5 minutes ago by
mawigoj318
• 0
0
votes
0
replies
185
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Ram
43k • written 4 days ago by
yifangt86
▴ 60
0
votes
0
replies
185
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
4 days ago by
Nitin
• 0
0
votes
0
replies
182
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 4 days ago by
Ram
43k • written 4 days ago by
mja
• 0
1
vote
0
replies
534
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
4 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
192
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 4 days ago by
Ram
43k • written 4 days ago by
Dinmukhamed
• 0
0
votes
0
replies
173
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
4 days ago by
DanielEB_fisk
▴ 20
0
votes
0
replies
205
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
3 days ago by
abhishekghadge
• 0
0
votes
0
replies
190
views
miRDeep2: How to get the read counts
mirdeep2
5 days ago by
Atul K.
• 0
0
votes
0
replies
128
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
3 days ago by
Mamatha Y S
• 0
129 results • Page
3 of 3
Recent Votes
Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
A: Finding the centromere and telomere of cattle genome (Bos Taurus)
A: How to systematically check if a bam file is truncated
Comment: some error in building kraken2 database
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
C: RSeQC Output from infer_experiment.py - what does it mean?
Recent Locations •
All
USA,
1 minute ago
Russia,
2 minutes ago
Australia,
2 minutes ago
Greece,
4 minutes ago
United States,
5 minutes ago
Netherlands,
6 minutes ago
Greenland,
7 minutes ago
Recent Awards •
All
Popular Question
to
sehriban.buyukkilic
▴ 10
Popular Question
to
O.rka
▴ 710
Popular Question
to
Akash D
▴ 40
Teacher
to
ATpoint
82k
Popular Question
to
subhiksha
▴ 30
Popular Question
to
v.berriosfarias
▴ 140
Popular Question
to
AdviceSeeker
• 0
Recent Replies
Comment: To get p-values for the TPM
by
ATpoint
82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis
by
gv
• 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM
by
VITALA
• 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
dsull
★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file
by
samuelkalandarov2002
▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
by
b.contreras.moreira
▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Traffic: 2204 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