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91 results • Page
2 of 2
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Rank
Views
Votes
Replies
0
votes
0
replies
128
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
3 days ago by
Jacob
• 0
0
votes
1
reply
178
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
0
votes
3
replies
274
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 3 days ago by
GenoMax
142k • written 3 days ago by
kim
• 0
3
votes
7
replies
330
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 0
0
votes
0
replies
122
views
Using limma in methylation EM-seq?
EM-seq
methylation
4 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
122
views
Synteny analysis
bacterial
synteny
genome
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Namil
• 0
0
votes
4
replies
243
views
Genbank File Format
gbkformat
3 days ago by
alenew.am
• 0
0
votes
0
replies
221
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
4 days ago by
SSSJec
• 0
0
votes
3
replies
212
views
Software to separate reads from different individuals
software
development
nanopore
updated 3 days ago by
GenoMax
142k • written 4 days ago by
njornet
▴ 20
0
votes
0
replies
92
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
4 days ago by
David
• 0
0
votes
2
replies
211
views
How to update R on ubuntu
installation
update
R
apt-get
4 days ago by
Bosberg
▴ 50
0
votes
0
replies
103
views
LEfSe
LEfSe
4 days ago by
benkosta
• 0
0
votes
0
replies
88
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
4 days ago by
Sara
▴ 30
0
votes
2
replies
154
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
4 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
97
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
4 days ago by
atharvakarkare14
▴ 30
0
votes
2
replies
197
views
What should I consider as FASTA for dataset?
PDB
FASTA
3 days ago by
Nafi
• 0
0
votes
0
replies
158
views
Differential accessibility using DiffBinf
diffbind
4 days ago by
Shloka
• 0
0
votes
0
replies
94
views
vg call vs vg surject
vg
variation
graphs
updated 4 days ago by
GenoMax
142k • written 4 days ago by
aliraza3119
• 0
0
votes
1
reply
134
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Winter
• 0
0
votes
1
reply
206
views
Finding batch and outlayers
Pca
updated 4 days ago by
christopher medway
▴ 460 • written 4 days ago by
Tigran
• 0
2
votes
2
replies
197
views
PDB related issue
rcsb
pdb
updated 4 days ago by
noodle
▴ 580 • written 4 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 4 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
1
reply
168
views
Downloading full alignments from Pfam
pfam
updated 5 days ago by
GenoMax
142k • written 5 days ago by
bef1
• 0
0
votes
0
replies
121
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 4 days ago by
dariober
14k • written 5 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
299
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Francesco
▴ 10
0
votes
0
replies
137
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
5 days ago by
tnminh89
▴ 10
0
votes
0
replies
142
views
Filter low express genes in microarray data
microarray
5 days ago by
Chris
▴ 260
0
votes
0
replies
566
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
6 days ago by
biocellbio
• 0
0
votes
0
replies
176
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 6 days ago by
Ram
43k • written 7 days ago by
SineWave
• 0
0
votes
3
replies
301
views
Highest variable features in single cell data
single-cell
updated 6 days ago by
bk11
★ 2.4k • written 8 days ago by
carolofharvest
▴ 30
1
vote
3
replies
377
views
PCA plot
DESeq2
PCAplot
updated 4 days ago by
LauferVA
4.2k • written 8 days ago by
Aaliya
▴ 10
0
votes
5
replies
366
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 6 days ago by
Istvan Albert
100k • written 9 days ago by
sehriban.buyukkilic
▴ 10
1
vote
8
replies
447
views
Downsampling fastq file
downsample
fastq
2 days ago by
marco.barr
▴ 90
0
votes
10
replies
495
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 11 days ago by
Patadu94
• 0
1
vote
6
replies
289
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 59 minutes ago by
GenoMax
142k • written 18 days ago by
eebloom
▴ 80
0
votes
3
replies
331
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 4 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
2
votes
5
replies
929
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 3 days ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
0
votes
1
reply
536
views
HOMER on AWS
HOMER
updated 13 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
3 days ago by
anna
▴ 20
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 19 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 4 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
91 results • Page
2 of 2
Recent Votes
Answer: Does comparing two different groups to a common third group introduce bias in th
Comment: High Malat-1 expression in single cell data
Comment: High Malat-1 expression in single cell data
Print Differentially Expressed Exons From Dexseq Results
C: Print Differentially Expressed Exons From Dexseq Results
C: Print Differentially Expressed Exons From Dexseq Results
Answer: Please Explain Window Size and Step Size
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Recent Awards •
All
Popular Question
to
curious
▴ 750
Popular Question
to
M.
▴ 30
Student
to
carolofharvest
▴ 30
Commentator
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e.r.zakiev
▴ 210
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dsull
★ 6.0k
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eebloom
▴ 80
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ManuelDB
▴ 80
Recent Replies
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
Comment: Raw counts using stringtie
by
GenoMax
142k
> Error parsing strand from GFF line Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
Comment: High Malat-1 expression in single cell data
by
carolofharvest
▴ 30
Thank you for sharing. What are your thoughts on the genes Gm42418, AY036118, and Gm26917? Some articles suggest that clusters with an abu…
Comment: Do I need to go back and filter my long-reads?
by
GenoMax
142k
> I think I will filter the reads ultimately. If your data was not run and basecalled using the same exact version of pore/software for a…
Comment: Raw counts using stringtie
by
Ram
43k
What is `stringie.sh`? Try `./stringtie.sh -h` and then `more stringtie.sh`.
Comment: Do I need to go back and filter my long-reads?
by
Ram
43k
> I think you should have the right to delete a question you yourself have submitted If you were to talk to someone, can you make them for…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
★ 1.9k
I don't have any experience using `BRAKER2` so I cannot comment, but I would be extra careful about data you find on non-model organisms. T…
Comment: Differential Expression Analysis using DESeq2 in R
by
GenoMax
142k
You can copy and paste your code and then use `101010` button in the edit window to format it as text to keep it monospaced. For example …
Comment: Same sequencing sample in multiple lanes. How to analyse it?
by
ST
• 0
I guess this could really depend on the "counting" strategy, the library complexity and possible lane biases. If e.g., EM is used to guide…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
Vijith
▴ 30
Hi dthorbur, thanks for the response. I have run Augustus using Arabidopsis as a species. I would like to know about the suitability of usi…
Comment: How does gene length effect the number of reads mapped
by
dsull
★ 6.0k
Alicia Oshlack has done some cool work on this but even the plots in her papers show that TPMs sometimes overcorrect and the relationship i…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![The below image contains the code and result also.][1] [1]: /media/images/96562b96-d508-4f67-96d1-7c71aa17
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
My response above was actually partly inspired off of a reading of your paper :)
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