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82 results • Page
1 of 2
Sort: replies
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Views
Votes
Replies
0
votes
11
replies
547
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
5 days ago by
atowns21
• 0
0
votes
10
replies
473
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
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
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
1
vote
8
replies
426
views
Downsampling fastq file
downsample
fastq
1 day ago by
marco.barr
▴ 80
3
votes
7
replies
294
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
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
0
votes
5
replies
278
views
Telescope issue
Telescope
RNA-seq
updated 6 hours ago by
GenoMax
141k • written 1 day ago by
eleven11
• 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
5
replies
352
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 6 days ago by
GenoMax
141k • written 7 days ago by
Bertalan_Takacs
▴ 90
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
0
votes
4
replies
225
views
Genbank File Format
gbkformat
1 day ago by
alenew.am
• 0
1
vote
4
replies
125
views
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
2 hours ago by
nicole.kavanagh
• 0
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
3
replies
293
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
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
3
replies
253
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 1 day ago by
GenoMax
141k • written 2 days ago by
kim
• 0
0
votes
3
replies
234
views
KEGG Pathways
r
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
Sudip
• 0
1
vote
3
replies
363
views
PCA plot
DESeq2
PCAplot
updated 3 days ago by
LauferVA
4.2k • written 6 days ago by
Aaliya
▴ 10
1
vote
3
replies
220
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
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
2
votes
2
replies
187
views
PDB related issue
rcsb
pdb
updated 2 days ago by
noodle
▴ 580 • written 3 days ago by
Nafi
• 0
0
votes
2
replies
185
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 days ago by
Nafi
• 0
0
votes
2
replies
259
views
Annovar using R package
Annovar
gnomAD
R
6 days ago by
DKA
▴ 40
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
1
vote
2
replies
188
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
2
replies
233
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
10 hours ago by
Nafi
• 0
0
votes
2
replies
167
views
How to update R on ubuntu
installation
update
R
apt-get
2 days ago by
Bosberg
▴ 50
1
vote
2
replies
239
views
alignment result
RNA-seq
samtools
hisat2
6 days ago by
ahmad.sajad4541
• 0
0
votes
1
reply
137
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
updated 18 hours ago by
Ram
43k • written 21 hours ago by
rianna.collins
• 0
0
votes
1
reply
118
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 12 hours ago by
i.sudbery
19k • written 23 hours ago by
Edmond
• 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
1
reply
488
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 6 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
1
reply
128
views
unable to get feature count results
featureCounts
updated 1 day ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
1
reply
70
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 4 hours ago by
Ram
43k • written 6 hours ago by
ernestine.kubi
• 0
0
votes
1
reply
131
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 4 hours ago by
Adam
▴ 30 • written 1 day ago by
Ahiad Chen Zion
• 0
0
votes
1
reply
198
views
Finding batch and outlayers
Pca
updated 2 days ago by
christopher medway
▴ 450 • written 2 days ago by
Tigran
• 0
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
1
reply
158
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
1
vote
1
reply
175
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
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
266
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 18 hours ago by
Ram
43k • written 23 hours ago by
Dr Huma Naz
• 0
0
votes
0
replies
35
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 1 hour ago by
Ram
43k • written 2 hours ago by
Oscar
▴ 10
0
votes
0
replies
151
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
6 days ago by
Aspire
▴ 330
0
votes
0
replies
153
views
how to read graph_test output of monocle 3
monocle3
6 days ago by
synat.keam
▴ 100
1
vote
0
replies
168
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
0
votes
0
replies
156
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
6 days ago by
Emily
▴ 10
0
votes
0
replies
169
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
6 days ago by
avocado123
• 0
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
82 results • Page
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C: TOPGO- how to do GO enrichment using a custom go database?
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)?
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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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