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116,833 results • Page
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bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 30 minutes ago by
Ram
43k • written 55 minutes ago by
Matthew
• 0
0
votes
0
replies
9
views
Enhanced Volcano-Cut off
enhanced
foldchange
volcano
1 hour ago by
odi
▴ 10
0
votes
0
replies
11
views
Help with Biopython for Beginner
Python
FASTA
Biopython
ORF
Beginner
1 hour ago by
cput
• 0
0
votes
0
replies
13
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
1 hour ago by
asalimih
▴ 60
0
votes
4
replies
258
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
3 hours ago by
schmince
• 0
0
votes
1
reply
66
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
2 hours ago by
Prawesh
• 0
795
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
9
replies
1.4k
views
kinannote software installation problems
kinannote
updated 3 hours ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
1
reply
76
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 3 hours ago by
marco.barr
▴ 90 • written 6 hours ago by
elisheva
▴ 120
0
votes
0
replies
30
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 2 hours ago by
Ram
43k • written 6 hours ago by
mathavanbioinfo
▴ 90
0
votes
1
reply
171
views
Seurat V5 integration
Seurat
integration
updated 2 hours ago by
Ram
43k • written 3 days ago by
starswillfade
▴ 10
0
votes
2
replies
134
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 2 hours ago by
Ram
43k • written 16 hours ago by
Sumeet
• 0
0
votes
0
replies
46
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 2 hours ago by
Ram
43k • written 7 hours ago by
carlopecoraro2
★ 2.5k
4
votes
5
replies
3.3k
views
How to compare compare two Sam files to check mapping
alignment
updated 8 hours ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
0
votes
2
replies
85
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 8 hours ago by
GenoMax
142k • written 8 hours ago by
madders73
• 0
2
votes
1
reply
144
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
updated 8 hours ago by
Bastien Hervé
5.3k • written 12 hours ago by
mnx0723
• 0
3
votes
4
replies
3.9k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 hours ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
0
votes
3
replies
169
views
RNA seq analysis
DESeq
RNA-seq
updated 3 hours ago by
Ram
43k • written 11 hours ago by
prifa
• 0
10
votes
3
replies
240
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 12 hours ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
ijarne
• 0
0
votes
0
replies
86
views
Chance for trained without experience
bio
updated 12 hours ago by
ATpoint
82k • written 12 hours ago by
shehab
• 0
1
vote
2
replies
128
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
13 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
63
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
13 hours ago by
Omics data mining
▴ 260
0
votes
2
replies
119
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
12 hours ago by
njornet
▴ 20
0
votes
2
replies
133
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 6 hours ago by
Adam
▴ 30 • written 14 hours ago by
Darya
• 0
0
votes
5
replies
183
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 11 hours ago by
Joe
21k • written 14 hours ago by
Lemonhope
• 0
0
votes
0
replies
80
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
14 hours ago by
Winter
• 0
0
votes
5
replies
225
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
8 hours ago by
me
• 0
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 15 hours ago by
DGTool
• 0 • written 4.8 years ago by
ww22runner
▴ 60
2
votes
1
reply
86
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
17 hours ago by
analyst
▴ 50
0
votes
0
replies
56
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
17 hours ago by
analyst
▴ 50
0
votes
0
replies
53
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
17 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
57
views
Blog:
Overview of Nanopore Sequencing
biotech
17 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
68
views
meffil.snp.concordance
meffil
methylation
snp_concordance
22 hours ago by
kyj222637
• 0
0
votes
1
reply
106
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 8 hours ago by
Bastien Hervé
5.3k • written 23 hours ago by
sooni
▴ 20
1
vote
5
replies
373
views
HCL database download
HCL
updated 22 hours ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
1
reply
222
views
barcode of TCR-sequencing
barcode
updated 1 day ago by
mizraelson
▴ 60 • written 8 days ago by
yueli7
▴ 250
0
votes
3
replies
169
views
STAR aligner error
RNA-seq
STAR
slurm
updated 3 hours ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
0
replies
73
views
monocle 3-- Could not get node in small cluster
monocle3
1 day ago by
synat.keam
▴ 100
0
votes
2
replies
161
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
8 hours ago by
Nicholas
• 0
1
vote
4
replies
325
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
1 day ago by
heelpPlease
• 0
0
votes
7
replies
403
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 6 hours ago by
Wayne
★ 2.0k • written 2 days ago by
JACKY
▴ 140
0
votes
0
replies
93
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
442
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 1 day ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
150
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Sony
▴ 10
5
votes
5
replies
248
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
20 hours ago by
Chris
▴ 280
0
votes
2
replies
158
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 6 hours ago by
swbarnes2
14k • written 1 day ago by
ahmad.sajad4541
• 0
1
vote
5
replies
193
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
145
views
student
epitranscriptomics
updated 1 day ago by
ATpoint
82k • written 1 day ago by
useriwa
• 0
0
votes
0
replies
97
views
Imputation of missing genotypes
panel
beagle
imputation
1 day ago by
analyst
▴ 50
0
votes
3
replies
159
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
116,833 results • Page
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Recent Votes
Verify if all the components of a pathway are present in a genomes
removeBatchEffect explained using base R linear models
How to get number of characters (nucleotides) in fasta file
Answer: How can I analyze normalized expression data?
A: How to append the cell barcode and UMI information to the fastq header in paired
Answer: Decoding MM and ML tags in .SAM file
C: salmon quantification vs. star mapping
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Recent Replies
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
I probably got some of the vocabulary wrong. I thought that "Dom HOR2932 HOR3036 HOR3726 KWSBambina Rec S42IL_124" were representing my ge…
Comment: featureCounts output assigned value higher than and HISAT2 mapping.
by
Ram
43k
It's featureCount**s**, not featureCount. I've edited your post and fixed all mentions of featureCounts.
Comment: kinannote software installation problems
by
Emanoelle
• 0
Hey, I know it's been 5 years but I have the same issue. When I run the test the software is unable to perform and always deliver the follo…
Comment: STAR aligner error
by
Ram
43k
If they can't help you, we probably can't do much either. But we can optimize your STAR command. BAM SortedByCoordinate is the worst settin…
Answer: Obtaining Infinium Methylation450K manifest for hg38
by
marco.barr
▴ 90
Hi, you can check it from github here: [https://zwdzwd.github.io/InfiniumAnnotation][1]. I don't know if this is what you are looking fo…
Comment: RNA seq analysis
by
ATpoint
82k
It makes absolutely no sense to conduct such an analysis. I strongly discourage you to even start with it. Results will be utterly nonsense…
Comment: Differentail gene expression results
by
swbarnes2
14k
Cross-posted: https://support.bioconductor.org/p/9158194/
Answer: Seurat V5 integration
by
Bastien Hervé
5.3k
It will depend on your context and question. I guess you will want to compare gene expression between your conditions within cell types …
Answer: Error in plotting PCA plot in seurat
by
Adam
▴ 30
You get this error when you try to compare two data frames that have different dimensions. Try using the traceback() command to figure out …
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
Sorry, this was supposed to be a comment appended to the chain above. I didn't mean to post as an answer.
Comment: Exploring Diet Effects in Single-Cell RNA Sequencing
by
Adam
▴ 30
> when I looked at the expression of aging marker genes, I noticed that diets sequenced in the same batch appeared more similar. How simil…
Answer: How to compare compare two Sam files to check mapping
by
DavidStreid
▴ 90
Curious if others have also benefited from Picard's [CompareSAMs][1] tool. Seems to do exactly what Madhu has requested. If the headers …
Answer: How/where can I get fungal mitogenome data for analysis?
by
alex.zaccaron
▴ 410
The best repository is probably NCBI Organelle Resources. You can search by taxonomy and download their mt genomes. Check it out for fungi…
Answer: How/where can I get fungal mitogenome data for analysis?
by
GenoMax
142k
Good place to start looking: https://www.ncbi.nlm.nih.gov/genome/organelle/ Mitochondrial genomes may also be included in full genomes so …
Comment: Correlating Bulk Differential Expression with quantitative
by
Nicholas
• 0
Thank you! I will give it a shot
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