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174 results • Page
2 of 4
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Votes
Replies
0
votes
0
replies
135
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
2 days ago by
O.rka
▴ 710
0
votes
1
reply
500
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 2 days ago by
Ram
43k • written 2 days ago by
Dr Huma Naz
• 0
2
votes
2
replies
255
views
p-value in CIBERSORT
CIBERSORT
p-value
2 days ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
337
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
eleven11
• 0
5
votes
6
replies
496
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 2 days ago by
me
▴ 760 • written 3 days ago by
Mariana
▴ 40
1
vote
1
reply
216
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 2 days ago by
Ram
43k • written 2 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
272
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
1 day ago by
Nafi
• 0
1
vote
3
replies
260
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
210
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 2 days ago by
GenoMax
142k • written 3 days ago by
Dora
▴ 10
0
votes
0
replies
154
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 2 days ago by
Ram
43k • written 2 days ago by
Chakri
• 0
0
votes
1
reply
168
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
Ahiad Chen Zion
• 0
1
vote
5
replies
270
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
41 minutes ago by
Riccardo
▴ 10
0
votes
0
replies
122
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
121
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 2 days ago by
Alexandros
• 0
0
votes
1
reply
157
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
3
replies
262
views
KEGG Pathways
r
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Sudip
• 0
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 2 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
124
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
2 days ago by
Bine
▴ 60
0
votes
1
reply
273
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
3 days ago by
David Langenberger
11k
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
3 days ago by
8armed
• 0
0
votes
1
reply
176
views
Deseq2
Deseq2
updated 3 days ago by
Jack Tierney
▴ 360 • written 3 days ago by
Sudip
• 0
1
vote
1
reply
210
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 3 days ago by
Michael
54k • written 3 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
255
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 3 days ago by
Lluís R.
★ 1.2k • written 3 days ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
184
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Sudip
• 0
1
vote
2
replies
213
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 3 days ago by
Ravita
• 0
0
votes
0
replies
107
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
3 days ago by
Adyasha
• 0
0
votes
0
replies
110
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
3 days ago by
fanglujing
▴ 60
0
votes
0
replies
125
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
3 days ago by
Jacob
• 0
0
votes
3
replies
730
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 3 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
259
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 3 days ago by
Ram
43k • written 3 days ago by
Hamtaro
▴ 50
0
votes
1
reply
178
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
0
votes
3
replies
271
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
kim
• 0
3
votes
2
replies
367
views
Extract protein sequence
fasta
alignment
blast
2 days ago by
anna
▴ 20
3
votes
3
replies
311
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 3 days ago by
noodle
▴ 580 • written 4 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
164
views
metagenomic virome quality assessment
viromics
metagenomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Petchimuthu
• 0
3
votes
7
replies
324
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 0
0
votes
0
replies
122
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
576
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
3 days ago by
e.r.zakiev
▴ 210
0
votes
0
replies
121
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
4
replies
241
views
Genbank File Format
gbkformat
3 days ago by
alenew.am
• 0
0
votes
5
replies
403
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
dsull
★ 5.9k • written 17 days ago by
bioinfo
▴ 150
0
votes
0
replies
221
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
3 days ago by
SSSJec
• 0
0
votes
3
replies
209
views
Software to separate reads from different individuals
software
development
nanopore
updated 3 days ago by
GenoMax
142k • written 3 days ago by
njornet
▴ 20
0
votes
0
replies
92
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
4
votes
5
replies
291
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 3 days ago by
dsull
★ 5.9k • written 3 days ago by
carolofharvest
▴ 10
0
votes
2
replies
208
views
How to update R on ubuntu
installation
update
R
apt-get
3 days ago by
Bosberg
▴ 50
4
votes
0
replies
130
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
3 days ago by
Biostar
2.7k
1
vote
1
reply
135
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Ruqaiya
• 0
0
votes
1
reply
272
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 3 days ago by
trausch
★ 1.9k • written 20 days ago by
zec018
• 0
174 results • Page
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Answer: How many reads for WGS Sequencing?
Answer: How many reads for WGS Sequencing?
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
Answer: how to split multi-fasta file into single fasta file named by header
How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
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Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This only works for the first line of sequences.
Answer: What purposes can TPM values be used for?
by
b.contreras.moreira
▴ 180
In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
alifafiq1
• 0
Thank you @AT point. I was planning to use DESeq2 and use the alternate hypothesis (lessAbs) too considering that is the only package that …
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
Comment: HOMER on AWS
by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly
by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
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Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
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