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82 results • Page
1 of 2
Sort: Votes
Rank
Views
Votes
Replies
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
2 days ago by
anna
▴ 20
3
votes
7
replies
295
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
2
votes
2
replies
187
views
PDB related issue
rcsb
pdb
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
Nafi
• 0
2
votes
5
replies
919
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 2 days ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
1
vote
2
replies
235
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
12 hours ago by
Nafi
• 0
1
vote
3
replies
364
views
PCA plot
DESeq2
PCAplot
updated 3 days ago by
LauferVA
4.2k • written 6 days ago by
Aaliya
▴ 10
1
vote
2
replies
239
views
alignment result
RNA-seq
samtools
hisat2
6 days ago by
ahmad.sajad4541
• 0
1
vote
0
replies
169
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
6 days ago by
rohitsatyam102
▴ 850
1
vote
2
replies
190
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
1
vote
4
replies
129
views
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
3 hours ago by
nicole.kavanagh
• 0
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 2 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
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
1
vote
8
replies
426
views
Downsampling fastq file
downsample
fastq
1 day ago by
marco.barr
▴ 80
1
vote
3
replies
222
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 1 day ago by
GenoMax
141k • written 1 day ago by
jeffrey.maurer.informatics
• 0
1
vote
1
reply
176
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 1 day ago by
Ram
43k • written 1 day ago by
Jonathan Yoou
▴ 60
1
vote
3
replies
281
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
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
5
replies
350
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
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
1
reply
162
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
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
1
reply
198
views
Finding batch and outlayers
Pca
updated 2 days ago by
christopher medway
▴ 450 • written 3 days ago by
Tigran
• 0
0
votes
2
replies
141
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
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
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
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
168
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
319
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
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
3
replies
194
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
185
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 days ago by
Nafi
• 0
0
votes
1
reply
159
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
0
votes
0
replies
111
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
1 day ago by
Jacob
• 0
0
votes
0
replies
94
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
91
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
1 day ago by
Adyasha
• 0
0
votes
4
replies
225
views
Genbank File Format
gbkformat
1 day ago by
alenew.am
• 0
0
votes
0
replies
104
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
1 day ago by
8armed
• 0
0
votes
10
replies
474
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 9 days ago by
Patadu94
• 0
0
votes
0
replies
99
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
95
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
0
votes
3
replies
254
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 1 day ago by
GenoMax
141k • written 2 days ago by
kim
• 0
82 results • Page
1 of 2
Recent Votes
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Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
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Comment: What does 'bundle_uuid' refer to in this metadata sheet?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
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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…
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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…
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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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