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50 results • Page
1 of 1
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Votes
Replies
0
votes
1
reply
1
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IGV interpretation for ATM gene for chromosome 11 for a deceased partient
IGV
variant
gene
just now by
mikemakaveli1
• 0
0
votes
1
reply
17
views
Raw counts using stringtie
stringtie
RNA-seq
analysis
counts
raw
30 minutes ago by
ahmad.sajad4541
• 0
0
votes
2
replies
48
views
Differential Expression Analysis using DESeq2 in R
Bioinformatics
analysis
R
deseq2
39 minutes ago by
Erina
• 0
0
votes
0
replies
9
views
Modify plot R mtDNA indel
plot
mtDNA
R
43 minutes ago by
marco.barr
▴ 90
0
votes
0
replies
11
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
50 minutes ago by
NorbertK
• 0
2
votes
2
replies
79
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 1 hour ago by
t.montserrat.ayuso
▴ 10 • written 4 hours ago by
carolofharvest
▴ 30
7
votes
7
replies
329
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 39 minutes ago by
dsull
★ 5.9k • written 4 days ago by
carolofharvest
▴ 30
0
votes
0
replies
17
views
WGCNA Module-Trait Heatmap
module_trait_heatmap
wgcna
heatmap
1 hour ago by
mja
• 0
0
votes
1
reply
42
views
Downloading older version of a tool
Alignment
tools
updated 2 hours ago by
GenoMax
142k • written 2 hours ago by
Ruqaiya
• 0
0
votes
0
replies
30
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
3 hours ago by
rustykb
▴ 20
1
vote
1
reply
59
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 4 hours ago by
ATpoint
82k • written 4 hours ago by
adi.gershon1
• 0
3
votes
5
replies
111
views
Generating mpileup file using samtools
mpileup
samtools
updated 2 hours ago by
Joe
21k • written 5 hours ago by
Ruqaiya
• 0
0
votes
5
replies
215
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 6 hours ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
JH
• 0
0
votes
3
replies
160
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 6 hours ago by
ATpoint
82k • written 16 hours ago by
Qi
• 0
0
votes
0
replies
45
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
7 hours ago by
Amos Bairoch
▴ 120
0
votes
1
reply
77
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 1 hour ago by
dthorbur
★ 1.9k • written 8 hours ago by
Vijith
▴ 30
0
votes
0
replies
65
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
9 hours ago by
Jeyong
• 0
0
votes
2
replies
648
views
homer not configured properly
Homer
makeTagDirectory
updated 11 hours ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
161
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 11 hours ago by
Alex Reynolds
35k • written 18 hours ago by
SJP
• 0
0
votes
0
replies
60
views
Empty table plot using plotGseaTable()
FGSEA
16 hours ago by
Chris
▴ 260
0
votes
1
reply
106
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 18 hours ago by
anovak
▴ 120 • written 22 hours ago by
Hang
• 0
1
vote
3
replies
153
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 18 hours ago by
jared.andrews07
★ 16k • written 21 hours ago by
yvonneh
▴ 10
1
vote
2
replies
130
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
updated 18 hours ago by
GenoMax
142k • written 18 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 19 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
116
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
19 hours ago by
dtnondorf
• 0
0
votes
1
reply
142
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 11 hours ago by
Chris Dean
▴ 390 • written 20 hours ago by
sovrappensiero
▴ 90
1
vote
2
replies
150
views
RNA-seq data for deep learning classification
rna-seq
2 hours ago by
Yuju
• 0
2
votes
6
replies
260
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
13 hours ago by
Qroid
▴ 40
0
votes
1
reply
464
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 22 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
101
views
Provean help
variant
Provean
updated 19 hours ago by
Mensur Dlakic
★ 27k • written 22 hours ago by
Arun Sai Kumar
• 0
1
vote
1
reply
120
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 23 hours ago by
bk11
★ 2.4k • written 1 day ago by
Jeol
▴ 20
1
vote
1
reply
129
views
Super ehancers
enhancers
updated 23 hours ago by
jared.andrews07
★ 16k • written 1 day ago by
Oburah
• 0
0
votes
6
replies
187
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated just now by
dsull
★ 5.9k • written 1 day ago by
Chen
• 0
1
vote
7
replies
385
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
3 hours ago by
eebloom
▴ 80
3
votes
3
replies
223
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 4 hours ago by
ATpoint
82k • written 1 day ago by
alifafiq1
• 0
0
votes
0
replies
82
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 22 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
104
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 22 hours ago by
Ram
43k • written 1 day ago by
4r-rtg
• 0
1
vote
1
reply
122
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 22 hours ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 90
9
votes
10
replies
440
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 22 hours ago by
Zamin Iqbal
▴ 20 • written 1 day ago by
nicole.kavanagh
• 0
1
vote
3
replies
199
views
Odd alignment question/finding
Alignment
updated 5 hours ago by
barslmn
★ 2.1k • written 1 day ago by
poordumbsillyidiot
• 0
0
votes
7
replies
494
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 13 hours ago by
LChart
3.9k • written 3 days ago by
kl
▴ 10
0
votes
1
reply
769
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 22 hours ago by
Ram
43k • written 2.7 years ago by
carov
• 0
1
vote
5
replies
293
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
5 hours ago by
Riccardo
▴ 10
0
votes
5
replies
277
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 6 hours ago by
Mohamed Abderrahmane
▴ 20 • written 4 days ago by
matteo.levorato
• 0
1
vote
4
replies
263
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
3 hours ago by
eebloom
▴ 80
1
vote
2
replies
260
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
3 hours ago by
eebloom
▴ 80
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 21 hours ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
0
votes
1
reply
535
views
HOMER on AWS
HOMER
updated 11 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
16
votes
12
replies
7.3k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 5 hours ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 17 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
50 results • Page
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Recent Votes
How to interpret DEXseq results in therms of significance
Answer: High Malat-1 expression in single cell data
Understanding ATAC-seq data
High Malat-1 expression in single cell data
Answer: DSEQ2 analysis
High Malat-1 expression in single cell data
Convert vcf files with phased genotypes to standard haplotype format
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Recent Replies
Answer: IGV interpretation for ATM gene for chromosome 11 for a deceased partient
by
mikemakaveli1
• 0
how can I interpret the mutation for the gene of ATM
Comment: How does gene length effect the number of reads mapped
by
dsull
★ 5.9k
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: Raw counts using stringtie
by
ahmad.sajad4541
• 0
![stringtie error][1] [1]: /media/images/6475a009-e1a6-412b-8515-a8aec173
Answer: 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
★ 5.9k
My response above was actually partly inspired off of a reading of your paper :)
Comment: Differential Expression Analysis using DESeq2 in R
by
ATpoint
82k
> everything is showing equal in environment section. But when I am checking for equalities, it’s showing False No idea what this means. P…
Answer: Analysis of intronic reads included scRNA-seq data
by
t.montserrat.ayuso
▴ 10
You can calculate the percentage of intronic reads for each cell using the [DropletQC][1] package for R. In this preprint we discuss th…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
I did say almost - obviously things are going to get tricky at gene ends - this is why we have the concept of effective length. Its interst…
Answer: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 10
Malat1 correlates with the intronic content and can be used as a nuclear indicator. In this preprint we discuss about this artifact and the…
Comment: How does gene length effect the number of reads mapped
by
dsull
★ 5.9k
I wouldn't say it's true that number of reads is linearly proportional to the length of the gene. That's just an assumption that people mak…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
★ 1.9k
Using any of the species present would likely result in a resonable annotation set. You could use *Arabidopsis* since it likely has the mos…
Comment: Downloading older version of a tool
by
GenoMax
142k
Have you tried conda install <pkg>=<version> so conda install smalt=0.5.8 <!-- junk -->
Comment: Generating mpileup file using samtools
by
Joe
21k
Older versions of software are usually available via distribution tools or the websites. It may require a lot of digging, but its almost ce…
Comment: RNA-seq data for deep learning classification
by
Yuju
• 0
Thank you very much for sharing your advice. Yes, it definitely makes sense that with the use of deep learning, models would learn normalis…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I didn't use the same tool as in the paper...
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