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175 results • Page
1 of 4
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0
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0
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6
views
WGCNA Module-Trait Heatmap
module_trait_heatmap
wgcna
heatmap
5 minutes ago by
mja
• 0
0
votes
1
reply
28
views
Downloading older version of a tool
Alignment
tools
updated 31 minutes ago by
GenoMax
142k • written 1 hour ago by
Ruqaiya
• 0
0
votes
0
replies
20
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
2 hours ago by
rustykb
▴ 20
2
votes
1
reply
50
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
carolofharvest
▴ 10
0
votes
1
reply
47
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 3 hours ago by
ATpoint
82k • written 3 hours ago by
adi.gershon1
• 0
3
votes
5
replies
87
views
Generating mpileup file using samtools
mpileup
samtools
updated 40 minutes ago by
Joe
21k • written 4 hours ago by
Ruqaiya
• 0
0
votes
5
replies
207
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 4 hours ago by
b.contreras.moreira
▴ 180 • written 22 hours ago by
JH
• 0
0
votes
3
replies
154
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 5 hours ago by
ATpoint
82k • written 15 hours ago by
Qi
• 0
0
votes
0
replies
40
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
6 hours ago by
Amos Bairoch
▴ 120
0
votes
1
reply
64
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 19 minutes ago by
dthorbur
★ 1.9k • written 6 hours ago by
Vijith
▴ 30
0
votes
0
replies
57
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
8 hours ago by
Jeyong
• 0
0
votes
2
replies
646
views
homer not configured properly
Homer
makeTagDirectory
updated 9 hours ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
159
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 10 hours ago by
Alex Reynolds
35k • written 17 hours ago by
SJP
• 0
0
votes
0
replies
57
views
Empty table plot using plotGseaTable()
FGSEA
15 hours ago by
Chris
▴ 260
0
votes
1
reply
103
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 16 hours ago by
anovak
▴ 120 • written 20 hours ago by
Hang
• 0
1
vote
3
replies
151
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 16 hours ago by
jared.andrews07
★ 16k • written 20 hours ago by
yvonneh
▴ 10
1
vote
2
replies
128
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
updated 16 hours ago by
GenoMax
142k • written 17 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 18 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
113
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
18 hours ago by
dtnondorf
• 0
0
votes
1
reply
138
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 10 hours ago by
Chris Dean
▴ 390 • written 19 hours ago by
sovrappensiero
▴ 90
1
vote
2
replies
140
views
RNA-seq data for deep learning classification
rna-seq
1 hour ago by
Yuju
• 0
2
votes
6
replies
255
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
12 hours ago by
Qroid
▴ 40
0
votes
1
reply
461
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 21 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
99
views
Provean help
variant
Provean
updated 18 hours ago by
Mensur Dlakic
★ 27k • written 21 hours ago by
Arun Sai Kumar
• 0
1
vote
1
reply
118
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 21 hours ago by
bk11
★ 2.4k • written 1 day ago by
Jeol
▴ 20
1
vote
1
reply
125
views
Super ehancers
enhancers
updated 21 hours ago by
jared.andrews07
★ 16k • written 1 day ago by
Oburah
• 0
0
votes
4
replies
156
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated just now by
dsull
★ 5.9k • written 23 hours ago by
Chen
• 0
5
votes
5
replies
212
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 22 hours ago by
atharvakarkare14
▴ 30 • written 1 day ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
375
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
1 hour ago by
eebloom
▴ 80
3
votes
3
replies
215
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 3 hours ago by
ATpoint
82k • written 1 day ago by
alifafiq1
• 0
0
votes
0
replies
75
views
Use of annotation of integrated Seurat object in single sample
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
76
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 21 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
196
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
101
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 21 hours ago by
Ram
43k • written 1 day ago by
4r-rtg
• 0
1
vote
1
reply
120
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 21 hours ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 90
0
votes
0
replies
73
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
1 day ago by
Rhiannon
• 0
0
votes
0
replies
82
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
1 day ago by
Vijith
▴ 30
9
votes
10
replies
437
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 21 hours ago by
Zamin Iqbal
▴ 20 • written 1 day ago by
nicole.kavanagh
• 0
0
votes
1
reply
257
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 1 day ago by
Scooter
▴ 280 • written 7 days ago by
avocado123
• 0
0
votes
0
replies
83
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
1 day ago by
James
▴ 10
0
votes
1
reply
571
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 1 day ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
196
views
Odd alignment question/finding
Alignment
updated 3 hours ago by
barslmn
★ 2.1k • written 1 day ago by
poordumbsillyidiot
• 0
0
votes
1
reply
188
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 1 day ago by
GenoMax
142k • written 1 day ago by
mgranada3
▴ 30
0
votes
0
replies
84
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
1 day ago by
meck
• 0
0
votes
0
replies
115
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 1 day ago by
Ram
43k • written 1 day ago by
Oscar
▴ 10
0
votes
7
replies
489
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 12 hours ago by
LChart
3.9k • written 3 days ago by
kl
▴ 10
0
votes
1
reply
203
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
J
• 0
1
vote
3
replies
282
views
DESeq2 processing problems
deseq2
R
updated 1 day ago by
ATpoint
82k • written 2 days ago by
jagdish7921
• 0
0
votes
1
reply
769
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 21 hours ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
132
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 1 day ago by
Ram
43k • written 1 day ago by
ernestine.kubi
• 0
175 results • Page
1 of 4
Recent Votes
Convert vcf files with phased genotypes to standard haplotype format
Convert vcf files with phased genotypes to standard haplotype format
A: Convert vcf files with phased genotypes to standard haplotype format
How to extract haplotype data from phased bcf files
How to extract haplotype data from phased bcf files
Answer: RNA-seq data for deep learning classification
Answer: Analysis of intronic reads included scRNA-seq data
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Recent Replies
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...
Comment: read length in structural variant calling
by
eebloom
▴ 80
Yes good idea. I guess the quality of the SV calls and as a proxy for quality the length and distribution of variants called might be infor…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I just realised I didn't align my reads with the tools they used and used bowtie2 instead. I can't download the older version that is menti…
Comment: Downsampling long-read BAM files
by
eebloom
▴ 80
This is not what I needed for this particular use case, as capping the coverage would lose the information on regions of copy number amplif…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Apologies, I deleted the question as I wasn't sure it would be helpful to others and it didn't seem to have a clear answer, not to snub the…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Thanks, I think it would be a good idea to track the results downstream to look for batch effects. I think I will filter the reads ultimate…
Comment: Generating mpileup file using samtools
by
ATpoint
82k
Seconding this. Apply current best practices (which is bcftools mpileup followed by something I forgot, see bcftools manual for variant cal…
Answer: Analysis of intronic reads included scRNA-seq data
by
ATpoint
82k
By default in CellRanger (lets assume you have 10x data processed with it) intronic reads are included. What you get in your matrix.mtx fil…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
The number of reads for a gene is almost exactly linearly proportional to the length of the gene. In paired-end sequencing, we generally co…
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
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