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80 results • Page
1 of 2
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Views
Votes
Replies
0
votes
0
replies
9
views
Intraspecies genomic GO term count differences
GO
ontology
24 minutes ago by
taavi.riit
• 0
1
vote
3
replies
71
views
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 10 minutes ago by
GenoMax
141k • written 3 hours ago by
nicole.kavanagh
• 0
0
votes
1
reply
55
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 2 hours ago by
Ram
43k • written 4 hours ago by
ernestine.kubi
• 0
0
votes
0
replies
35
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
4 hours ago by
VITALA
• 0
0
votes
1
reply
132
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
updated 15 hours ago by
Ram
43k • written 18 hours ago by
rianna.collins
• 0
0
votes
1
reply
110
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 9 hours ago by
i.sudbery
19k • written 20 hours ago by
Edmond
• 0
0
votes
0
replies
84
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
20 hours ago by
O.rka
▴ 710
0
votes
1
reply
253
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 15 hours ago by
Ram
43k • written 20 hours ago by
Dr Huma Naz
• 0
0
votes
5
replies
258
views
Telescope issue
Telescope
RNA-seq
updated 3 hours ago by
GenoMax
141k • written 1 day ago by
eleven11
• 0
0
votes
0
replies
97
views
Defined objects of type "S4" error in single cell analysis
Seurat
single-cell
DoubletFinder
single-nuclei
SeuratObject
1 day ago by
sarphilsar
• 0
1
vote
1
reply
168
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 22 hours ago by
Ram
43k • written 1 day ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
224
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
8 hours ago by
Nafi
• 0
1
vote
3
replies
214
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
jeffrey.maurer.informatics
• 0
0
votes
1
reply
113
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 2 hours ago by
Adam
▴ 30 • written 1 day ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
91
views
barcode of TCR-sequencing
barcode
1 day ago by
yueli7
▴ 250
0
votes
0
replies
91
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 1 day ago by
Ram
43k • written 1 day ago by
Alexandros
• 0
0
votes
1
reply
125
views
unable to get feature count results
featureCounts
updated 1 day ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
0
replies
90
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
0
votes
3
replies
230
views
KEGG Pathways
r
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
Sudip
• 0
0
votes
0
replies
95
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
99
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
1 day ago by
8armed
• 0
1
vote
2
replies
185
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 1 day ago by
Ravita
• 0
0
votes
0
replies
87
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
1 day ago by
Adyasha
• 0
0
votes
0
replies
90
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
1 day ago by
fanglujing
▴ 60
0
votes
0
replies
106
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
1 day ago by
Jacob
• 0
0
votes
1
reply
155
views
Differential Accessibility
DiffBind
updated 1 day ago by
Ram
43k • written 1 day ago by
Shloka
• 0
0
votes
3
replies
248
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 1 day ago by
GenoMax
141k • written 2 days ago by
kim
• 0
3
votes
7
replies
287
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
113
views
Using limma in methylation EM-seq?
EM-seq
methylation
2 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
115
views
Synteny analysis
bacterial
synteny
genome
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Namil
• 0
0
votes
4
replies
224
views
Genbank File Format
gbkformat
1 day ago by
alenew.am
• 0
0
votes
0
replies
204
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
193
views
Software to separate reads from different individuals
software
development
nanopore
updated 2 days ago by
GenoMax
141k • written 2 days ago by
njornet
▴ 20
0
votes
0
replies
88
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
2 days ago by
David
• 0
0
votes
2
replies
162
views
How to update R on ubuntu
installation
update
R
apt-get
2 days ago by
Bosberg
▴ 50
0
votes
0
replies
94
views
LEfSe
LEfSe
2 days ago by
benkosta
• 0
0
votes
0
replies
80
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
0
votes
2
replies
140
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
2 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
95
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
2 days ago by
atharvakarkare14
▴ 20
0
votes
2
replies
185
views
What should I consider as FASTA for dataset?
PDB
FASTA
1 day ago by
Nafi
• 0
0
votes
0
replies
81
views
Differential accessibility using DiffBinf
diffbind
2 days ago by
Shloka
• 0
0
votes
0
replies
90
views
vg call vs vg surject
vg
variation
graphs
updated 2 days ago by
GenoMax
141k • written 2 days ago by
aliraza3119
• 0
0
votes
1
reply
120
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Winter
• 0
0
votes
1
reply
197
views
Finding batch and outlayers
Pca
updated 2 days ago by
christopher medway
▴ 450 • written 2 days ago by
Tigran
• 0
2
votes
2
replies
187
views
PDB related issue
rcsb
pdb
updated 2 days ago by
noodle
▴ 580 • written 2 days ago by
Nafi
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 2 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
1
reply
161
views
Downloading full alignments from Pfam
pfam
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bef1
• 0
0
votes
0
replies
115
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 2 days ago by
dariober
14k • written 3 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
280
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Francesco
▴ 10
0
votes
0
replies
134
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
3 days ago by
tnminh89
▴ 10
80 results • Page
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Recent Votes
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
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Recent Replies
Comment: Bacterial plasmid analysis
by
GenoMax
141k
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…
Comment: RNA editing sites based on DNA seq and RNA seq
by
Adam
▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject
by
Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
by
Adam
▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long
by
bkleiboeker
▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue
by
GenoMax
141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery
by
GenoMax
141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Comment: Telescope issue
by
eleven11
• 0
Thank you! how would I correct that?
Comment: DESeq2 processing problems
by
Ram
43k
This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
Comment: Post-imputation plot
by
kl
▴ 10
All of them are G/C and A/T variants Some seem mismatches based on AF and some seem to need flipping. I guess I am confused, as in the Mich…
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
Nafi
• 0
Thank you for the reply I have 16 gb of RAM then I can give a try then.
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