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187 results • Page
2 of 4
Sort: replies
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Views
Votes
Replies
0
votes
4
replies
340
views
Merge clusters in Seurat UMAP
seurat
umap
3 days ago by
kilcdincer
▴ 10
1
vote
4
replies
301
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
4 days ago by
Arton
▴ 10
0
votes
4
replies
248
views
Sequencing Depth (Read Depth) Calculations
depth
4 days ago by
LucisTheFather
• 0
0
votes
4
replies
334
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 3 days ago by
Tony
• 0 • written 4 days ago by
vk
▴ 10
3
votes
4
replies
415
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Pierre Lindenbaum
161k
0
votes
4
replies
288
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
2 days ago by
mavy
▴ 10
2
votes
4
replies
51
views
Filter Genome for Specific Sites
genomic
filtering
bedtools
updated 1 hour ago by
GenoMax
142k • written 1 hour ago by
Anita
• 0
0
votes
4
replies
350
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 2 days ago by
txema.heredia
▴ 130 • written 3 days ago by
Ngrin
• 0
1
vote
4
replies
364
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 6 days ago by
Ram
43k • written 11 days ago by
samRayne
• 0
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 6 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
3
replies
374
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
6 days ago by
mropri
▴ 150
0
votes
3
replies
200
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 6 days ago by
Ram
43k • written 7 days ago by
yau
• 0
3
votes
3
replies
298
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 6 days ago by
Ram
43k • written 20 days ago by
Adyasha
• 0
3
votes
3
replies
369
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 6 days ago by
Mathew
▴ 140 • written 9 days ago by
Christopher
• 0
0
votes
3
replies
359
views
Snakemake wrapper issue
fastqc
snakemake
updated 6 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
215
views
How to access GWAVA software of data
GWAVA
updated 6 days ago by
GenoMax
142k • written 6 days ago by
nonaddldy
▴ 10
0
votes
3
replies
225
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 6 days ago by
GenoMax
142k • written 6 days ago by
RNAseqer
▴ 270
2
votes
3
replies
292
views
Finding variants within a subset of a BAM file
variant
calling
6 days ago by
ramiro.barrantes
• 0
0
votes
3
replies
271
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 6 days ago by
noodle
▴ 580 • written 6 days ago by
doramora
▴ 10
2
votes
3
replies
222
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Prawesh
• 0
0
votes
3
replies
176
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
5 days ago by
Esraa
• 0
1
vote
3
replies
299
views
Using ggplotly in R
ggplot
ggplotly
updated 5 days ago by
jared.andrews07
★ 16k • written 6 days ago by
jen
▴ 10
1
vote
3
replies
211
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 5 days ago by
shpak.max
▴ 50
3
votes
3
replies
238
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Alexandra
• 0
3
votes
3
replies
252
views
getting exon coordinates
genomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Xbox_27
• 0
1
vote
3
replies
284
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 4 days ago by
GenoMax
142k • written 6 days ago by
ohtang7
▴ 40
1
vote
3
replies
806
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 4 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
3
replies
289
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 3 days ago by
Ram
43k • written 5 days ago by
kuttibiotech2009
▴ 30
2
votes
3
replies
258
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 3 days ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
3
replies
283
views
Sam file Header problem
Sam
Header
problem
file
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
saifulislam99121
• 0
0
votes
3
replies
206
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 6 hours ago by
GenoMax
142k • written 1 day ago by
KHURRAM SHAHZAD
• 0
0
votes
3
replies
131
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 3 hours ago by
Ram
43k • written 8 hours ago by
Bioinformatics_begginner
▴ 20
1
vote
3
replies
277
views
Super ehancers
enhancers
updated 3 hours ago by
GenoMax
142k • written 18 days ago by
Oburah
• 0
3
votes
2
replies
289
views
imputation through beagle
panel
beagle
reference
imputation
6 days ago by
analyst
▴ 50
0
votes
2
replies
251
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
melissachua90
▴ 70
1
vote
2
replies
703
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 1 day ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
0
votes
2
replies
222
views
How can I calculate the OS of each patient?
overall-survival
38 minutes ago by
Pedro
• 0
0
votes
2
replies
201
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
5 days ago by
melissa.joubert
• 0
0
votes
2
replies
302
views
Traveler with Infernal mapping failed
r2dt
updated 1 day ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
1
vote
2
replies
215
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 5 days ago by
colindaven
6.4k • written 5 days ago by
mbrav005
• 0
0
votes
2
replies
114
views
Error in using BioSampleParser tool: subscript out of bounds
R
2 hours ago by
Mohamed Samir
▴ 20
0
votes
2
replies
191
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
6 days ago by
IdaHao0921
• 0
1
vote
2
replies
272
views
How to interpret infinite odds ratio?
statistics
6 days ago by
Lukas
• 0
0
votes
2
replies
253
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 2 days ago by
LauferVA
4.2k • written 3 days ago by
ijarne
• 0
2
votes
2
replies
194
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 4 days ago by
Ram
43k • written 5 days ago by
jsmith120f
• 0
2
votes
2
replies
209
views
Genome Visualization Tools
bacterial
genome
updated 5 days ago by
GenoMax
142k • written 5 days ago by
dlera.lozano
▴ 10
0
votes
2
replies
244
views
Trimming tool
Trimmer
tool
updated 2 days ago by
ntsopoul
▴ 60 • written 3 days ago by
GeneC
• 0
2
votes
2
replies
276
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 days ago by
Ram
43k • written 4 days ago by
txema.heredia
▴ 130
0
votes
2
replies
214
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
16 hours ago by
Luqman
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 6 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
187 results • Page
2 of 4
Recent Votes
Answer: Filter Genome for Specific Sites
Answer: Filter Genome for Specific Sites
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
The Biostar Herald for Monday, May 20, 2024
Answer: Generating Group/Cluster Lists from fastq files
The Biostar Herald for Monday, May 20, 2024
ClusterProfiler : What is GeneRatio and BgRatio?
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Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient?
by
Pedro
• 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
Comment: Filter Genome for Specific Sites
by
Anita
• 0
Great, thank you!
Comment: Filter Genome for Specific Sites
by
Anita
• 0
This is unhelpful and doesn't answer my question.
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
Thank you so much for helping me out in this! I have used most of the sequences that are found in this table. But, some samples like the…
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa This table has the SR…
Comment: Filter Genome for Specific Sites
by
Pierre Lindenbaum
161k
> My sites are in an Excel file right now ![enter image description here][1] <!-- was an American educator and academic administrator…
Answer: Filter Genome for Specific Sites
by
GenoMax
142k
> I have a list of ~1,300 single bp sites Convert your file to plain text [**BED format**][1] (three fields required). Use `bedtools slo…
Comment: How to generate an Upset plot in R to plot the shared variants between cell free
by
sainavyav22
• 0
It worked, Thank you very much!
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm unsure you'll be able to identify whole chromosomes that are not core from illumina reads alone. That might be easier to do with a micr…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
Mohamed Samir
▴ 20
Dear marco, We need to ask ourselves why it is not working for all bioprojects ? I have looked into this, and observed that as long as the…
Comment: Why most genes have high padj values
by
Ram
43k
You ***want*** ~3000 DE genes?<a href="" title="Text added because biostars parser needs it"></a>
Answer: Generating Group/Cluster Lists from fastq files
by
GenoMax
142k
> I was hoping to just do this in galaxy This is not a galaxy option but `clumpify.sh ` from BBMap suite can cluster sequences/dedupe th…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
Hello, just wanted to check in if the code has been fixed yet? Thank you.
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