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177 results • Page
4 of 4
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101
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VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 14 hours ago by
anovak
▴ 120 • written 18 hours ago by
Hang
• 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
▴ 10
0
votes
0
replies
92
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
0
votes
2
replies
208
views
How to update R on ubuntu
installation
update
R
apt-get
3 days ago by
Bosberg
▴ 50
0
votes
0
replies
52
views
Empty table plot using plotGseaTable()
FGSEA
13 hours ago by
Chris
▴ 260
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
3 days ago by
SSSJec
• 0
0
votes
3
replies
330
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 3 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
0
votes
0
replies
121
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
0
replies
120
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 3 days ago by
dariober
14k • written 5 days ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
122
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
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
3 days ago by
Sara
▴ 30
0
votes
1
reply
133
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Winter
• 0
0
votes
0
replies
93
views
vg call vs vg surject
vg
variation
graphs
updated 3 days ago by
GenoMax
142k • written 4 days ago by
aliraza3119
• 0
0
votes
1
reply
164
views
metagenomic virome quality assessment
viromics
metagenomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Petchimuthu
• 0
0
votes
1
reply
272
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 3 days ago by
trausch
★ 1.9k • written 20 days ago by
zec018
• 0
0
votes
5
replies
404
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
dsull
★ 5.9k • written 17 days ago by
bioinfo
▴ 150
0
votes
0
replies
101
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
0
votes
2
replies
153
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
109
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
3
replies
209
views
Software to separate reads from different individuals
software
development
nanopore
updated 3 days ago by
GenoMax
142k • written 3 days ago by
njornet
▴ 20
0
votes
1
reply
206
views
Finding batch and outlayers
Pca
updated 4 days ago by
christopher medway
▴ 450 • written 4 days ago by
Tigran
• 0
0
votes
2
replies
197
views
What should I consider as FASTA for dataset?
PDB
FASTA
3 days ago by
Nafi
• 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
730
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 3 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
0
replies
125
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
3 days ago by
Jacob
• 0
0
votes
0
replies
110
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
3 days ago by
fanglujing
▴ 60
0
votes
4
replies
259
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 3 days ago by
Ram
43k • written 3 days ago by
Hamtaro
▴ 50
177 results • Page
4 of 4
Recent Votes
Answer: Controlling for FDR in 450k methylation microarray data
Comment: Generating mpileup file using samtools
Comment: Generating mpileup file using samtools
Answer: Downsampling long-read BAM files
Comment: Generating mpileup file using samtools
Answer: What analysis suitable to identify similarly expressed genes between two samples
Comment: What analysis suitable to identify similarly expressed genes between two samples
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Recent Replies
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. The tool isn't available on conda and I can't fi…
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 …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
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