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Limit : this week
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175 results • Page
3 of 4
Sort: Views
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Views
Votes
Replies
0
votes
1
reply
196
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
2
votes
2
replies
195
views
PDB related issue
rcsb
pdb
updated 4 days ago by
noodle
▴ 580 • written 4 days ago by
Nafi
• 0
1
vote
3
replies
195
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
2
votes
2
replies
186
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Sudip
• 0
1
vote
0
replies
184
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
1 day ago by
carlopecoraro2
★ 2.5k
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
1
reply
177
views
Deseq2
Deseq2
updated 3 days ago by
Jack Tierney
▴ 360 • written 3 days ago by
Sudip
• 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
0
replies
172
views
RNA-seq: full length gene
RNA-seq
updated 6 days ago by
Ram
43k • written 7 days ago by
Nargis
• 0
0
votes
1
reply
170
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Edmond
• 0
0
votes
1
reply
169
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
Ahiad Chen Zion
• 0
0
votes
1
reply
168
views
Downloading full alignments from Pfam
pfam
updated 4 days ago by
GenoMax
142k • written 5 days ago by
bef1
• 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
1
vote
1
reply
163
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
2 days ago by
heelpPlease
• 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
1
reply
158
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 3 days ago by
Ravita
• 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
0
votes
0
replies
155
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 2 days ago by
Ram
43k • written 2 days ago by
Chakri
• 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
2
replies
153
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
4 days ago by
Lluís R.
★ 1.2k
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
0
votes
0
replies
142
views
Filter low express genes in microarray data
microarray
5 days ago by
Chris
▴ 260
0
votes
1
reply
142
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 4 days ago by
i.sudbery
19k • written 4 days ago by
DOBI
• 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
1
reply
137
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Ruqaiya
• 0
1
vote
2
replies
136
views
RNA-seq data for deep learning classification
rna-seq
56 minutes ago by
Yuju
• 0
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
135
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
2 days ago by
O.rka
▴ 710
0
votes
1
reply
133
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
132
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 1 day ago by
Ram
43k • written 1 day ago by
ernestine.kubi
• 0
4
votes
0
replies
130
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
4 days ago by
Biostar
2.7k
0
votes
0
replies
128
views
Differential accessibility using DiffBinf
diffbind
4 days ago by
Shloka
• 0
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
0
votes
0
replies
126
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
3 days ago by
Jacob
• 0
0
votes
0
replies
124
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
3 days ago by
Bine
▴ 60
1
vote
1
reply
124
views
Super ehancers
enhancers
updated 21 hours ago by
jared.andrews07
★ 16k • written 1 day ago by
Oburah
• 0
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
3 days ago by
8armed
• 0
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
122
views
barcode of TCR-sequencing
barcode
3 days ago by
yueli7
▴ 250
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
121
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
121
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
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
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
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 3 days ago by
Alexandros
• 0
0
votes
0
replies
114
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
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
0
replies
111
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
0
replies
109
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
4 days ago by
carlopecoraro2
★ 2.5k
175 results • Page
3 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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