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1,103 results • Page
2 of 23
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Votes
Replies
1
vote
2
replies
207
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 1 day ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
0
replies
103
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
0
replies
106
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
0
votes
0
replies
122
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
3
replies
725
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 2 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
242
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 2 days ago by
Ram
43k • written 2 days ago by
Hamtaro
▴ 50
0
votes
1
reply
171
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
0
votes
3
replies
263
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 1 day ago by
GenoMax
142k • written 2 days ago by
kim
• 0
3
votes
2
replies
351
views
Extract protein sequence
fasta
alignment
blast
1 day ago by
anna
▴ 20
3
votes
3
replies
302
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 2 days ago by
noodle
▴ 580 • written 3 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
155
views
metagenomic virome quality assessment
viromics
metagenomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Petchimuthu
• 0
3
votes
7
replies
302
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
2 days ago by
salias
• 0
0
votes
0
replies
115
views
Using limma in methylation EM-seq?
EM-seq
methylation
2 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
563
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
2 days ago by
e.r.zakiev
▴ 200
0
votes
0
replies
117
views
Synteny analysis
bacterial
synteny
genome
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Namil
• 0
0
votes
4
replies
227
views
Genbank File Format
gbkformat
2 days ago by
alenew.am
• 0
0
votes
5
replies
387
views
How should I make kallisto indexes?
kallisto
updated 2 days ago by
dsull
★ 5.9k • written 16 days ago by
bioinfo
▴ 150
0
votes
0
replies
208
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
2 days ago by
SSSJec
• 0
0
votes
3
replies
200
views
Software to separate reads from different individuals
software
development
nanopore
updated 2 days ago by
GenoMax
142k • written 2 days ago by
njornet
▴ 20
0
votes
0
replies
89
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
2 days ago by
David
• 0
4
votes
5
replies
272
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 2 days ago by
dsull
★ 5.9k • written 2 days ago by
Kazo
▴ 10
0
votes
2
replies
175
views
How to update R on ubuntu
installation
update
R
apt-get
2 days ago by
Bosberg
▴ 50
4
votes
0
replies
121
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
2 days ago by
Biostar
2.7k
0
votes
1
reply
127
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 2 days ago by
GenoMax
142k • written 3 days ago by
Ruqaiya
• 0
0
votes
1
reply
270
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 2 days ago by
trausch
★ 1.9k • written 19 days ago by
zec018
• 0
0
votes
0
replies
98
views
LEfSe
LEfSe
2 days ago by
benkosta
• 0
0
votes
0
replies
81
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
2 days ago by
Sara
▴ 30
1
vote
4
replies
374
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
2 days ago by
hagl
▴ 10
0
votes
2
replies
174
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
1 day ago by
matteo.levorato
• 0
0
votes
2
replies
145
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
2 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
136
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
DOBI
• 0
0
votes
0
replies
96
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
3 days ago by
atharvakarkare14
▴ 20
5
votes
16
replies
659
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
3 days ago by
Ruqaiya
• 0
0
votes
2
replies
188
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 days ago by
Nafi
• 0
38
votes
24
replies
1.8k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
noodle
▴ 580
0
votes
0
replies
86
views
Differential accessibility using DiffBinf
diffbind
3 days ago by
Shloka
• 0
0
votes
0
replies
92
views
vg call vs vg surject
vg
variation
graphs
updated 2 days ago by
GenoMax
142k • written 3 days ago by
aliraza3119
• 0
0
votes
1
reply
124
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 2 days ago by
GenoMax
142k • written 3 days ago by
Winter
• 0
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 3 days ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
199
views
Finding batch and outlayers
Pca
updated 3 days ago by
christopher medway
▴ 450 • written 3 days ago by
Tigran
• 0
2
votes
2
replies
192
views
PDB related issue
rcsb
pdb
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
Nafi
• 0
0
votes
0
replies
107
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
407
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 1 day ago by
LauferVA
4.2k • written 3 days ago by
jinyu
▴ 10
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 3 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
441
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
3 days ago by
ashaneev07
▴ 20
0
votes
1
reply
163
views
Downloading full alignments from Pfam
pfam
updated 3 days ago by
GenoMax
142k • written 3 days ago by
bef1
• 0
0
votes
1
reply
743
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 3 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
284
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 3 days ago by
i.sudbery
19k • written 5 days ago by
vanbelj
▴ 40
0
votes
0
replies
115
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 2 days ago by
dariober
14k • written 4 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
285
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 3 days ago by
ATpoint
82k • written 4 days ago by
Francesco
▴ 10
1,103 results • Page
2 of 23
Recent Votes
Answer: Bacterial plasmid analysis
Define enhancer regions
A: how can i download human ribosomal reference ?
Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Discrepancy in read counts from fastq
R: Unable to use analyzeFeatures because argument is not a vector
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nicole.kavanagh
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Recent Replies
Answer: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Noone has an idea? Thank you!
Answer: Bacterial plasmid analysis
by
shenwei356
8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape?
by
Scooter
▴ 280
Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
Answer: Basic stats in hierfstat
by
mdav
• 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p
by
GenoMax
142k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
142k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems
by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
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