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696 results • Page
2 of 14
Sort: Votes
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Votes
Replies
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 24 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
4
votes
2
replies
286
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 23 days ago by
Ram
44k • written 25 days ago by
carolofharvest
▴ 40
4
votes
6
replies
12k
views
Looking for differential gene expression between treatment, within a specific cluster (seurat)
seurat
updated 1 day ago by
jared.andrews07
★ 17k • written 4.7 years ago by
cook.675
▴ 230
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 19 days ago by
Tawny
▴ 180 • written 3.1 years ago by
julia_geh
▴ 20
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 24 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
4
votes
1
reply
358
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 13 days ago by
dariober
14k • written 14 days ago by
Holly
▴ 30
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
28 days ago by
anna
▴ 20
4
votes
5
replies
501
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
29 days ago by
analyst
▴ 50
4
votes
1
reply
239
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
updated 4 days ago by
swbarnes2
14k • written 4 days ago by
May Ling
• 0
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 14 days ago by
Anitha
▴ 10 • written 5.1 years ago by
stephaniem
• 0
4
votes
3
replies
431
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 14 days ago by
Mathew
▴ 150 • written 17 days ago by
Christopher
▴ 10
4
votes
6
replies
437
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
4 days ago by
Shicheng Guo
★ 9.4k
4
votes
1
reply
282
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 22 days ago by
zx8754
11k • written 23 days ago by
Jautis
▴ 570
4
votes
0
replies
175
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
29 days ago by
Biostar
2.8k
4
votes
1
reply
375
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
28 days ago by
pairedttest
▴ 10
4
votes
5
replies
3.5k
views
How to compare compare two Sam files to check mapping
alignment
updated 19 days ago by
DavidStreid
▴ 90 • written 6.5 years ago by
madhu.9124
▴ 60
4
votes
6
replies
340
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
4 days ago by
bio_info
▴ 20
4
votes
7
replies
470
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
14 days ago by
Chen
• 0
4
votes
2
replies
217
views
Duplicated sequence samtools
bowtie2
samtools
updated 14 days ago by
GenoMax
142k • written 14 days ago by
Moinuddin
• 0
4
votes
2
replies
247
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
salmon
updated 11 hours ago by
Ram
44k • written 3 days ago by
Tonya S.
▴ 10
4
votes
9
replies
677
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 7 days ago by
marco.barr
▴ 130 • written 12 days ago by
diqixiaoyaoer
▴ 20
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 20 days ago by
chenl
▴ 10 • written 2.6 years ago by
Martyna
• 0
4
votes
2
replies
303
views
GRCh38.gmap file
gnomix
gmap
23 days ago by
lorena9132
▴ 10
4
votes
9
replies
555
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
11 days ago by
Gabriel R.
★ 2.9k
4
votes
3
replies
3.0k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 19 days ago by
Pierre Lindenbaum
162k • written 19 days ago by
Lila M
★ 1.3k
4
votes
1
reply
233
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
13 days ago by
J.
▴ 40
3
votes
2
replies
448
views
Extract protein sequence
fasta
alignment
blast
27 days ago by
anna
▴ 20
3
votes
7
replies
453
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
28 days ago by
Sergio A.S.
• 0
3
votes
4
replies
369
views
Truncated metadata file report from ENA Portal API
ena
python
17 days ago by
Giulia
• 0
3
votes
2
replies
206
views
vg autoindex seems stuck after a week of running
vg
pangenome
6 hours ago by
StevieP
▴ 10
3
votes
3
replies
340
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 17 days ago by
Ram
44k • written 18 days ago by
Omics data mining
▴ 260
3
votes
4
replies
514
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 21 days ago by
Gordon Smyth
★ 7.2k • written 24 days ago by
SHN
▴ 40
3
votes
10
replies
5.3k
views
6 follow
txt file to bigwig
MEME
bigwig
updated 16 hours ago by
ATpoint
82k • written 8.6 years ago by
tanni93
▴ 50
3
votes
8
replies
885
views
Random Access remote BAM files
htslib
BAM
updated 5 days ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
3
votes
3
replies
308
views
what is another word for a BLAST "hit"?
blast
alignment
17 days ago by
dec986
▴ 380
3
votes
5
replies
488
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
7 days ago by
beantkapoor16
▴ 10
3
votes
4
replies
355
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
2 days ago by
Alexandra
• 0
3
votes
6
replies
559
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 15 days ago by
Pine
▴ 20 • written 22 days ago by
snajafy
• 0
3
votes
5
replies
453
views
Super ehancers
enhancers
updated 6 days ago by
jared.andrews07
★ 17k • written 26 days ago by
Oburah
• 0
3
votes
2
replies
299
views
imputation through beagle
panel
beagle
reference
imputation
14 days ago by
analyst
▴ 50
3
votes
8
replies
770
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 21 days ago by
Chris Dean
▴ 410 • written 25 days ago by
sovrappensiero
▴ 100
3
votes
0
replies
130
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 6 days ago by
Ram
44k • written 6 days ago by
Rafael Soler
★ 1.2k
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 20 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
4
replies
219
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
1 day ago by
MboiTui
▴ 20
3
votes
3
replies
318
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 14 days ago by
Ram
44k • written 28 days ago by
Adyasha
• 0
3
votes
5
replies
392
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 2 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
QX
• 0
3
votes
2
replies
230
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 15 days ago by
ATpoint
82k • written 15 days ago by
jennyp0706
• 0
3
votes
1
reply
228
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 18 days ago by
dthorbur
★ 2.0k • written 18 days ago by
Eren
• 0
3
votes
4
replies
500
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 4 days ago by
fracarb8
★ 1.7k • written 11 days ago by
txema.heredia
▴ 130
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
23 days ago by
Ibrahim Tanyalcin
★ 1.2k
696 results • Page
2 of 14
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Comment: Confirmation required on how DiffBind generates union of regions (min. 1bp overl
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Tagging: https://www.biostars.org/u/10855/ <!-- this is -->
Answer: Best practices in Fungal Genome Assembly
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Then how it will be supporting risk snps in individual patient sample? and so it is like a population based study. could you please make a…
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142k
> assuming its impossible to calculate insert size when paired end reads do not overlap in an RNA library If you have a reference availabl…
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How to make sure the larger rRNAs are included?
Comment: Error with pheatmap - 'from' must be a finite number
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Please report ``` all(is.finite(mat.z)) all(is.finite(dist(mat.z))) pheatmap(mat.z, cluster_rows = FALSE, cluster_cols = FALSE) pheatmap(ma…
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It might be worth trying to cluster sequences with a few intermediate species too. Then the centroid of the cluster can theoretically be on…
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> any(is.infinite(mat.z)) [1] FALSE
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vmpsb
• 0
Thanks, how should I proceed?
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Difference is that plotting Z-scores plots each group and logFC plots differences between groups. Simply a different way of showing things.…
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> I am asking this particular question due that I am used to work with bulk RNAseq data and I usually consider a gene is worth to focus in …
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Are there already annotations published for the genome? If so, I doubt there is a dedicated tool since this is a simple task of parsing the…
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Errors and warnings are clear, we can reproduce them with this simple example Somewhere *pheatmap* is getting a minimum value excluding NA…
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A single PRS number is meaningless without background data like 1000 genomes, UK Biobank, etc.
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