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82 results • Page
2 of 2
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0
votes
0
replies
153
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
5 days ago by
turcoa1
• 0
1
vote
0
replies
156
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
5 days ago by
KABILAN
▴ 70
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
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
562
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
0
replies
136
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
0
replies
81
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
0
replies
95
views
LEfSe
LEfSe
2 days ago by
benkosta
• 0
0
votes
0
replies
91
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
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
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
0
replies
116
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
0
replies
112
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
1 day ago by
Jacob
• 0
0
votes
0
replies
95
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
92
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
1 day ago by
Adyasha
• 0
0
votes
0
replies
105
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
1 day ago by
8armed
• 0
0
votes
0
replies
100
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
96
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
97
views
barcode of TCR-sequencing
barcode
1 day ago by
yueli7
▴ 250
0
votes
0
replies
96
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
0
replies
104
views
Defined objects of type "S4" error in single cell analysis
Seurat
single-cell
DoubletFinder
single-nuclei
SeuratObject
1 day ago by
sarphilsar
• 0
0
votes
0
replies
89
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
1 day ago by
O.rka
▴ 710
0
votes
0
replies
47
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
8 hours ago by
VITALA
• 0
0
votes
0
replies
25
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
4 hours ago by
meck
• 0
0
votes
0
replies
32
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 2 hours ago by
Ram
43k • written 3 hours ago by
mgranada3
▴ 30
0
votes
0
replies
149
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
6 days ago by
4fzcgueyp5
• 0
82 results • Page
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Comment: What does 'bundle_uuid' refer to in this metadata sheet?
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Recent Replies
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…
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.
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