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117,476 results • Page
4 of 2350
Sort: Rank
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Views
Votes
Replies
3
votes
5
replies
333
views
assemble extracted kmers into longer contigs/sequences
assembly
unique
kmers
8 days ago by
sapuizait
▴ 10
3
votes
4
replies
326
views
Error: Trimmomatic Command not found
NGS
Illumina
Quality-Control
Trimmomatic
updated 9 days ago by
Ram
44k • written 9 days ago by
Tundup
• 0
0
votes
1
reply
226
views
single nucleus RNA seq processing pipeline questions
demultiplexing
snRNAseq
updated 9 days ago by
dsull
★ 6.2k • written 9 days ago by
biotrekker
▴ 100
0
votes
0
replies
186
views
Add gene expression boxplot from plotCounts to each row of oncoprint via ComplexHeatmap
R
ComplexHeatmap
oncoprint
updated 9 days ago by
Ram
44k • written 9 days ago by
bioinfo8
▴ 230
0
votes
1
reply
221
views
Hybrid ScRNA Seq genome (transcriptome
scrna
10x
cellranger
updated 8 days ago by
dsull
★ 6.2k • written 9 days ago by
Kay
• 0
0
votes
1
reply
202
views
Fastqc: kmer-content failed
fastqc
kmer
updated 9 days ago by
Ram
44k • written 9 days ago by
Joseph
• 0
5
votes
5
replies
440
views
Home made clustering
R
clustering
9 days ago by
Bastien Hervé
5.4k
4
votes
9
replies
563
views
How to solve Freebayes memory issue
NGS
freebayes
SNP
8 days ago by
anikcropscience
▴ 260
5
votes
3
replies
339
views
chIP-seq vs ATACseq analysis
ATACseq
6 days ago by
QX
▴ 20
0
votes
0
replies
379
views
How to calculate the P-distance in Heteroplasmy Analysis Using mtDNA PacBio Data: Tools and Procedures
pacBio
Heteroplasmy
Somatic-mutations
mtDNA
updated 8 days ago by
Ram
44k • written 9 days ago by
hashim.rana11
▴ 20
1
vote
1
reply
235
views
Fastq files from control WGS X30 samples, Illumina Novaseq 6000
dna-seq
wgs
fastq
updated 8 days ago by
Ram
44k • written 9 days ago by
damian.loska
▴ 20
1
vote
2
replies
292
views
cancer type prediction based on RNASeq gene expression data?
cancer
RNA-seq
updated 8 days ago by
Ram
44k • written 9 days ago by
J.F.Jiang
▴ 930
0
votes
3
replies
257
views
Nextflow pipeline - GATK error
nextflow
applyBQSR
gatk
updated 9 days ago by
Pierre Lindenbaum
162k • written 9 days ago by
eesha28112001
• 0
0
votes
1
reply
206
views
invalid class “Assay” object issue from Seurat
seurat
updated 9 days ago by
bk11
★ 2.7k • written 9 days ago by
QX
▴ 20
8
votes
3
replies
318
views
conda-like env for R
R
conda
updated 6 days ago by
dthorbur
★ 2.0k • written 9 days ago by
QX
▴ 20
2
votes
3
replies
333
views
r script for wgcna analysis
microarray
wgcna
updated 9 days ago by
andres.firrincieli
3.6k • written 9 days ago by
Ruchi
▴ 10
0
votes
3
replies
312
views
scRNA integration problem with cluster not being separated
Seurat
scRNA
updated 6 days ago by
QX
▴ 20 • written 9 days ago by
mnx0723
• 0
0
votes
0
replies
168
views
Conservation score calculation
Conservation-score
10 days ago by
Varsha
• 0
0
votes
0
replies
159
views
Fusion Gene Primer
FusionGene
qPCR
primer
10 days ago by
IVORY
• 0
5
votes
4
replies
416
views
Basic question about lncRNA identification
lncRNA
10 days ago by
ZZOYEA
▴ 20
1
vote
3
replies
302
views
Can I go from kallisto results to SEURAT directly
cell
bustoolls
kallisto
single
updated 7 days ago by
dsull
★ 6.2k • written 10 days ago by
biotrekker
▴ 100
0
votes
5
replies
387
views
How to know protomter position in the chromosome?
ATAC-seq
updated 7 days ago by
rfran010
▴ 960 • written 10 days ago by
sunyeping
▴ 110
2
votes
4
replies
1.1k
views
Need to create a small artificial SRA file for unit testing
sequencing
sequence
4.3 years ago by
Sean McCorkle
▴ 20
6
votes
4
replies
344
views
Normalization of samples with very different transcriptomic profiles
DESeq2
normalization
RNA-seq
edgeR
DGE
updated 5 days ago by
ATpoint
83k • written 10 days ago by
paulanavarrete116
• 0
0
votes
4
replies
307
views
Test custom signature using GSEA in scRNA-seq
scRNA-seq
Seurat
GSEA
9 days ago by
bio_info
▴ 20
1
vote
2
replies
254
views
Question about protein-peptide docking
active-site
docking
updated 9 days ago by
Mensur Dlakic
★ 27k • written 10 days ago by
Acervo
• 0
4
votes
6
replies
453
views
SortmeRNA command of the latest version does not work
metatranscriptomics
sortmerna
updated 10 days ago by
Ram
44k • written 14 days ago by
eimanpharmacist
▴ 20
0
votes
0
replies
165
views
Genome mapping mm39 via GTK (BaseRecalibration) - Where to get known sites of polymorphisms?
mm39
10 days ago by
Rashid
• 0
0
votes
0
replies
161
views
Value of short kmer lengths with 300PE sequencing
metagenomics
sequencing
spades
microbiome
10 days ago by
Bryan
▴ 10
0
votes
0
replies
161
views
News:
Online course: Reproducibility Data Analysis with R, from 28-31 October
R
Git
Quarto
Reproducibility
Docker
updated 10 days ago by
Ram
44k • written 10 days ago by
carlopecoraro2
★ 2.5k
0
votes
3
replies
243
views
Bcftools consensus unexpected output
Bcftools
updated 10 days ago by
Ram
44k • written 10 days ago by
selplat21
▴ 20
0
votes
8
replies
805
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 10 days ago by
Ram
44k • written 5 weeks ago by
ajbarrett98
• 0
1
vote
3
replies
344
views
Genomic coordinates in the BioNano VCF
bionano
VCF
SMAP
optical_genome_mapping
updated 6 days ago by
cmdcolin
★ 3.8k • written 11 days ago by
avigail.shnaider
• 0
1
vote
3
replies
500
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 10 days ago by
Pierre Lindenbaum
162k • written 4 weeks ago by
Arton
▴ 10
0
votes
0
replies
139
views
Genetic DIversity Of Macrolide-Resistant Shigella species
comparative-genomics
prokka
updated 10 days ago by
Ram
44k • written 10 days ago by
eduardooseigyimah
• 0
3
votes
2
replies
903
views
Non-symmetric shrinkage with apeglm?
RNA-Seq
DESeq2
apeglm
updated 10 days ago by
Ram
44k • written 3.3 years ago by
Chris-OHRI
▴ 30
0
votes
6
replies
674
views
I am trying to get my head around amplicon sequencing library prep but can't understand how the adapters are attached
library-preparation
illumina
amplicon
updated 10 days ago by
Ram
44k • written 10 days ago by
ScottDansk
▴ 10
0
votes
0
replies
130
views
Paired snATACseq and snRNAseq over multiple tissues - best approaches
Signac
ArchR
Seurat
ATACseq
10 days ago by
matt.a.bennett25890
▴ 30
0
votes
7
replies
454
views
How do I update the gene names of TCGA data correctly?
HGNC
TCGA
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 11 days ago by
Ivana
• 0
0
votes
1
reply
196
views
Atac seq Annotation
Atac-seq
Signac
Seurat
updated 10 days ago by
ATpoint
83k • written 11 days ago by
yau
• 0
2
votes
1
reply
194
views
Correct pvalue threshold for a GWAS analysis on mitochondrial variants with PLINK2
mitochondria
gwas
p-value
plink2
updated 10 days ago by
Ram
44k • written 10 days ago by
padrebio
▴ 10
0
votes
0
replies
138
views
MToolBox: cat: test.lst: No such file or directory
MToolBox
updated 10 days ago by
Ram
44k • written 10 days ago by
Stavroula
• 0
0
votes
1
reply
210
views
Query regarding single cell rna seq annotation using marker genes
scRNA-seq
updated 10 days ago by
Ram
44k • written 11 days ago by
sc_analysis
• 0
0
votes
1
reply
653
views
Building a mappability mask with SNPable
SNPable
mappability
samtools
updated 11 days ago by
oviscandensis
• 0 • written 10 months ago by
biostars
▴ 10
4
votes
8
replies
452
views
BAM File Quality Sequences Are "?" and File Size is Very Small After STAR Alignment
Bam
Fastq
Gene-expression
RNA-seq
updated 10 days ago by
Ram
44k • written 11 days ago by
Tommmm
• 0
0
votes
1
reply
164
views
Bismark Methylation calling
Bismark
Methylation
WGBS
updated 10 days ago by
Ram
44k • written 11 days ago by
Keem Uarren Eiryll
• 0
2
votes
4
replies
350
views
Differential gene expression
Differential-gene-expression
10 days ago by
goyal.shiwali
▴ 10
0
votes
0
replies
134
views
Why Does Metalign Relative Abundance Change?
metagenomics
metalign
11 days ago by
echolley
• 0
1
vote
5
replies
349
views
Question about CIBERSORTx Docker to Singularity
CIBERSORTx
docker
singularity
updated 11 days ago by
Ram
44k • written 12 days ago by
jinghuang800
▴ 10
4
votes
0
replies
201
views
Herald:
The Biostar Herald for Wednesday, June 05, 2024
herald
11 days ago by
Biostar
2.9k
117,476 results • Page
4 of 2350
Recent Votes
A: What Control For Chip-Seq: Input, Igg Or Untagged Strain?
A: anlysing ChIPSeq without input
A: Human dna reference file with no prefix 'chr'
How to convert old entrez id to updated-entrez id in R?
Answer: Example human WGS fastq data
Answer: NCBI vs Ensembl - Ortholog genes Information
Answer: NCBI vs Ensembl - Ortholog genes Information
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Recent Replies
Answer: How to measure pairwise genetic distance in all samples of a VCF file
by
hewm2008
▴ 40
you can try this tools :https://github.com/BGI-shenzhen/VCF2Dis
Comment: How to download a file from zenodo link without leaving terminal?
by
GenoMax
143k
You have tried to log in with one of the methods mentioned (ORCID/GitHub or a local Zenodo account) and that did not work?
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
yes, this seems to be the problem. I will try realigning to a version of hg38 without alt contigs.
Comment: Removing batch effect in time-series data
by
Álvaro
• 0
I performed a clustered heatmap and PCA for all samples and the different timepoints did not group together. However, my doubts come from a…
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
Strange, I wonder why. Could it have anything to do with the "chr20_KI270871v1_alt"?
Comment: BCFtools not calling variant, despite adequate coverage
by
Pierre Lindenbaum
162k
your read is discarded because mapping quality=0
Answer: Removing batch effect in time-series data
by
rfran010
▴ 960
Have you performed more formal analysis? PCA, clustering, correlation, etc... If you have a time dependent batch effect, I would expect …
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
I uploaded the sam file here if you want to take a look: https://github.com/samtools/bcftools/issues/2211
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
The reads are not duplicates. I think the color might be due to also matching the chr20 alt contig but I'm not sure. An example line from …
Comment: How to download a file from zenodo link without leaving terminal?
by
SlowSD
• 0
Okay, are you aware of any file access setting in zenodo by changing which this can work out?
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
The output is: chr20 63439704 G 23 ,,,,,aa,.A.A,,a,a.aA.aA FFFFFFFFkFFFFFFFFFFFFFF
Comment: How to download a file from zenodo link without leaving terminal?
by
Pierre Lindenbaum
162k
https://zenodo.org/records/11791175 > The record is publicly accessible, but files are restricted to users with access. so, no.
Comment: Problem in input data loading in Structure
by
Mensur Dlakic
★ 27k
Error messages are usually meant to be taken literally. It says that your first line has two fewer columns than the rest of your file. It p…
Comment: How to download a file from zenodo link without leaving terminal?
by
SlowSD
• 0
Still, a 6kb html file gets downloaded in the name of SRR396636.sra_1.fastq
Comment: How to download a file from zenodo link without leaving terminal?
by
Medhat
9.7k
Could you try `wget -L -O SRR396636.sra_1.fastq "https://zenodo.org/record/11791175/files/SRR396636.sra_1.fastq"`
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