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186 results • Page
2 of 4
Sort: Votes
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Views
Votes
Replies
1
vote
0
replies
173
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
2 days ago by
eebloom
▴ 80
1
vote
10
replies
864
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 5 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
1
vote
11
replies
5.5k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 5 days ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
1
vote
7
replies
492
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 1 day ago by
Pierre Lindenbaum
161k • written 4 days ago by
schmince
• 0
1
vote
7
replies
494
views
Question regarding WGCNA
WGCNA
Network-construction
2 days ago by
deepak
• 0
1
vote
9
replies
341
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 4 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
4
replies
475
views
cellranger error message
multiplexing
cellranger
updated 1 day ago by
Max
• 0 • written 12 weeks ago by
Alivia
▴ 10
1
vote
4
replies
364
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
4 days ago by
heelpPlease
• 0
1
vote
2
replies
210
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 2 days ago by
Michael
54k • written 2 days ago by
ashaneev07
▴ 20
1
vote
2
replies
175
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
4 days ago by
robert.flynn.21
• 0
1
vote
1
reply
434
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 2 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
1
vote
0
replies
146
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
5 days ago by
Biostar
2.7k
1
vote
0
replies
127
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
2 days ago by
Shae
▴ 10
1
vote
4
replies
388
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 1 day ago by
GenoMax
142k • written 24 days ago by
aniigodwinn
• 0
1
vote
4
replies
288
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
22 hours ago by
rackbersingh
• 0
1
vote
3
replies
301
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
6 days ago by
Lada
▴ 30
1
vote
1
reply
259
views
Seurat V5 integration
Seurat
integration
updated 2 days ago by
Ram
43k • written 6 days ago by
starswillfade
▴ 10
1
vote
5
replies
390
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by
Ram
43k • written 6 days ago by
snajafy
• 0
1
vote
3
replies
180
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 22 hours ago by
Ram
43k • written 1 day ago by
Omics data mining
▴ 260
1
vote
1
reply
213
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 4 days ago by
Michael
54k • written 4 days ago by
Guillermo
• 0
1
vote
0
replies
152
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 5 days ago by
zx8754
11k • written 8 days ago by
Emilie
▴ 10
1
vote
3
replies
152
views
Tassel 5 GBS: Is there something wrong with my fastqs?
tassel
fastq
gbs
updated 20 hours ago by
GenoMax
142k • written 22 hours ago by
meck
• 0
1
vote
0
replies
127
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
sarumonsus
▴ 10
1
vote
1
reply
135
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 2 days ago by
andres.firrincieli
3.6k • written 2 days ago by
kacollier
▴ 30
1
vote
2
replies
1.6k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 2 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
1
vote
1
reply
163
views
student
epitranscriptomics
updated 4 days ago by
ATpoint
82k • written 4 days ago by
useriwa
• 0
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
6 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
2
replies
145
views
Genome Assembly task + Protein Translation, assignment advice on a question
sequence-analysis
protein-synthesis
9 hours ago by
rackbersingh
• 0
1
vote
2
replies
418
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
2 days ago by
Zeng Hao
▴ 40
1
vote
5
replies
413
views
HCL database download
HCL
updated 3 days ago by
Ram
43k • written 7 days ago by
sooni
▴ 20
1
vote
2
replies
257
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 4 days ago by
Weiwen
• 0 • written 5 days ago by
MICOS
▴ 10
1
vote
3
replies
227
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 2 days ago by
GenoMax
142k • written 2 days ago by
cput
• 0
1
vote
5
replies
320
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 5 days ago by
Ram
43k • written 5 days ago by
snajafy
• 0
1
vote
2
replies
232
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 5 days ago by
zx8754
11k • written 5 days ago by
snajafy
• 0
1
vote
2
replies
316
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
5 days ago by
M.
▴ 30
1
vote
6
replies
693
views
anRichment is missing
WGCNA
anRichment
updated 5 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
0
votes
0
replies
79
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
1 day ago by
beantkapoor16
• 0
0
votes
2
replies
257
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 1 day ago by
GenoMax
142k • written 7 days ago by
Ximena
• 0
0
votes
1
reply
146
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 1 day ago by
curious
▴ 750 • written 1 day ago by
SeoGyun
• 0
0
votes
2
replies
178
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 22 hours ago by
Ram
43k • written 2 days ago by
sainavyav22
• 0
0
votes
1
reply
116
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 22 hours ago by
Ram
43k • written 1 day ago by
Shwetha
• 0
0
votes
0
replies
83
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 22 hours ago by
Ram
43k • written 1 day ago by
naomiboldon
• 0
0
votes
0
replies
111
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
updated 20 hours ago by
GenoMax
142k • written 9 days ago by
meck
• 0
0
votes
10
replies
320
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
updated 20 hours ago by
swbarnes2
14k • written 1 day ago by
Tuck898
• 0
0
votes
0
replies
74
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
17 hours ago by
Christopher
• 0
0
votes
4
replies
250
views
Correlation Analysis
statistics
methylation
NGS
expression
11 hours ago by
Researcher
▴ 30
0
votes
2
replies
177
views
How are score_weights calculated in this code?
single-cell
10 hours ago by
carolofharvest
▴ 40
0
votes
0
replies
48
views
imputation through beagle
panel
beagle
reference
imputation
9 hours ago by
analyst
▴ 50
0
votes
0
replies
48
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
8 hours ago by
beginner123
• 0
0
votes
1
reply
77
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
updated 7 hours ago by
Pierre Lindenbaum
161k • written 10 hours ago by
analyst
▴ 50
186 results • Page
2 of 4
Recent Votes
A: VCF files: Change Chromosome Notation
VCF files: Change Chromosome Notation
VCF files: Change Chromosome Notation
Answer: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
Answer: Failed to open VCF file
Answer: Failed to open VCF file
Merging public vcf files: <NON_REF> in ALT
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Recent Replies
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Thank you Pierre, I am going to take some time to get my head around this and report back if it works.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Thanks for the crosspost! Just trying to get things figured out.
Answer: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
ATpoint
82k
To the best of my knowledge, CIBERSORT is and has always and only been available via the official website application from Stanford. Whatev…
Comment: BioLabDonkey - new Mac program for molecular biologists
by
vytarasov
▴ 180
Update of BioLabDonkey - Version 5.6 - In silico PCR function is added.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
cross posted: https://stackoverflow.com/questions/78462732/ > Please mind that posting the same question to multiple sites can be perceive…
Comment: java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
by
Pierre Lindenbaum
161k
command is missing, version is missing.
Answer: Failed to open VCF file
by
Pierre Lindenbaum
161k
> Error: Failed to open vcf file Fixing: No such file or directory one of your file is missing, obviously. Check files exist using `[…
Comment: Align paired and unpaired reads simultaneously using Bowtie2?
by
Ruqaiya
• 0
I have forward reads that didn't require any trimming except for adapter sequence. but the reverse read file required trimming so i trimmed…
Comment: Trimmomatic: What is the difference between paired and unpaired output files in
by
Ruqaiya
• 0
can we not mention unpaired ? i have a reverse read file that needs a lot of trimming but forward file is usable. I don't understand how to…
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
by
rackbersingh
• 0
It is an indeed an old assignment question, I am doing revision and practicing answering questions for an upcoming test and just wanted to …
Comment: How are score_weights calculated in this code?
by
carolofharvest
▴ 40
I've found this code [in this site :][1] . It doesn't seem like they've shared any additional information about this in the previous line…
Comment: Correlation Analysis
by
Researcher
▴ 30
Thank you so much. I ran based on the above code and found that all gene columns have the same values, which you obtain as the average corr…
Answer: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
use bcftools merge with --force-samples and then use jvarkit https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ to replace the no-call …
Answer: In IGV is this a heterogeneous mutation or false call?
by
swbarnes2
14k
Since all the reads that show the alternate allele have to be clipped to align there, I'd say those reads are misaligned. I would say that…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
> Here's a few lines from the head of the raw fastq If your files are actually compressed (as their names suggest) then you should not be …
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