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163 results • Page
3 of 4
Sort: Votes
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Votes
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0
votes
2
replies
288
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 6 days ago by
GenoMax
141k • written 6 days ago by
Begonia_pavonina
▴ 150
0
votes
1
reply
218
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 6 days ago by
ATpoint
82k • written 6 days ago by
AaronJaime
• 0
0
votes
0
replies
163
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 6 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
260
views
Annovar using R package
Annovar
gnomAD
R
6 days ago by
DKA
▴ 40
0
votes
0
replies
163
views
Designing single-stable RNA molecules
structure
RNA
6 days ago by
Edna
• 0
0
votes
0
replies
173
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
6 days ago by
simplitia
▴ 130
0
votes
11
replies
552
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
6 days ago by
atowns21
• 0
0
votes
0
replies
153
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
6 days ago by
turcoa1
• 0
0
votes
0
replies
200
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
5 days ago by
HarperReed
• 0
0
votes
0
replies
170
views
RNA-seq: full length gene
RNA-seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Nargis
• 0
0
votes
3
replies
296
views
Highest variable features in single cell data
single-cell
updated 5 days ago by
bk11
★ 2.4k • written 6 days ago by
Kazo
▴ 10
0
votes
2
replies
277
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 5 days ago by
Ram
43k • written 6 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
174
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 5 days ago by
Ram
43k • written 5 days ago by
SineWave
• 0
0
votes
0
replies
565
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
5 days ago by
biocellbio
• 0
0
votes
2
replies
249
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
4 days ago by
Guille
• 0
0
votes
5
replies
353
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 4 days ago by
Istvan Albert
100k • written 7 days ago by
sehriban.buyukkilic
▴ 10
0
votes
2
replies
336
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 4 days ago by
Jesse
▴ 740 • written 6 days ago by
Broccoli
• 0
0
votes
1
reply
321
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Jesse
▴ 740 • written 12 days ago by
yifangt86
▴ 60
0
votes
0
replies
138
views
Filter low express genes in microarray data
microarray
4 days ago by
Chris
▴ 260
0
votes
0
replies
134
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
4 days ago by
tnminh89
▴ 10
0
votes
1
reply
742
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
0
votes
1
reply
163
views
Downloading full alignments from Pfam
pfam
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bef1
• 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
0
replies
84
views
Differential accessibility using DiffBinf
diffbind
2 days ago by
Shloka
• 0
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
1
reply
133
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
DOBI
• 0
0
votes
1
reply
199
views
Finding batch and outlayers
Pca
updated 2 days ago by
christopher medway
▴ 450 • written 3 days ago by
Tigran
• 0
0
votes
0
replies
106
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
142
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
97
views
LEfSe
LEfSe
2 days ago by
benkosta
• 0
0
votes
1
reply
269
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
1
reply
126
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Ruqaiya
• 0
0
votes
0
replies
92
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
122
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
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
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
0
votes
2
replies
171
views
How to update R on ubuntu
installation
update
R
apt-get
2 days ago by
Bosberg
▴ 50
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
320
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 2 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
0
votes
0
replies
117
views
Synteny analysis
bacterial
synteny
genome
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Namil
• 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
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
1
reply
153
views
metagenomic virome quality assessment
viromics
metagenomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Petchimuthu
• 0
0
votes
5
replies
386
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
3
replies
196
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
2
replies
186
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 days ago by
Nafi
• 0
0
votes
1
reply
168
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
0
votes
3
replies
722
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
0
replies
117
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
0
replies
100
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
163 results • Page
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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?
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Recent Replies
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
141k
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
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…
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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…
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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…
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141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
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