Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
185 results • Page
2 of 4
Sort: Votes
Rank
Views
Votes
Replies
1
vote
2
replies
212
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
3 days ago by
ojaswinipandey
• 0
1
vote
6
replies
373
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
3 days ago by
Umer
▴ 50
1
vote
1
reply
186
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 5 days ago by
ATpoint
82k • written 5 days ago by
rj.rezwan
• 0
1
vote
1
reply
215
views
constructing pangenome through psvcp
psvcp
pangenome
6 days ago by
analyst
▴ 50
1
vote
10
replies
624
views
Add stats to the plot
R
2 days ago by
Ghada
• 0
1
vote
2
replies
237
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
Dr.
• 0
1
vote
8
replies
501
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 6 days ago by
Alex Reynolds
35k • written 10 days ago by
ntsopoul
▴ 60
1
vote
2
replies
183
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 3 days ago by
Ram
44k • written 3 days ago by
Harshita
• 0
1
vote
2
replies
733
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 5 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
4
replies
359
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 6 days ago by
Joe
21k • written 15 days ago by
cput
• 0
1
vote
3
replies
908
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 1 day ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
1
vote
4
replies
395
views
some error in building kraken2 database
metagenome
kraken2
updated 1 day ago by
GenoMax
142k • written 4 weeks ago by
Art1ess
• 0
1
vote
2
replies
174
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
6 hours ago by
F110152169
• 0
1
vote
1
reply
124
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 1 day ago by
GenoMax
142k • written 1 day ago by
azeu
▴ 10
1
vote
2
replies
360
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 4 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
1
vote
3
replies
197
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 2 days ago by
GenoMax
142k • written 2 days ago by
s
• 0
1
vote
6
replies
299
views
samtools write-index
samtools
updated 1 day ago by
aw7
▴ 310 • written 2 days ago by
LucisTheFather
• 0
1
vote
2
replies
388
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 3 days ago by
finch
• 0 • written 3 months ago by
star
▴ 10
1
vote
4
replies
317
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 3 days ago by
Ram
44k • written 9 days ago by
Arton
▴ 10
1
vote
4
replies
276
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
2 days ago by
shpak.max
▴ 50
1
vote
3
replies
199
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 2 days ago by
Pierre Lindenbaum
162k • written 3 days ago by
mrk
• 0
1
vote
3
replies
229
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Wilber0x
▴ 50
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 5 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
1
reply
130
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 4 days ago by
GenoMax
142k • written 4 days ago by
niruf
• 0
1
vote
2
replies
196
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 4 days ago by
Ram
44k • written 4 days ago by
Sony
▴ 10
1
vote
3
replies
560
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 3 days ago by
Klaus S
▴ 160 • written 6 weeks ago by
Zeng Hao
▴ 40
1
vote
4
replies
160
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
1 hour ago by
sc_analysis
• 0
1
vote
3
replies
240
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 23 hours ago by
Jeremy
▴ 910 • written 1 day ago by
Mohamed Samir
▴ 30
0
votes
1
reply
101
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 1 day ago by
Ram
44k • written 1 day ago by
a.bibek52
▴ 10
0
votes
2
replies
172
views
What do the transcript variant # mean in RefSeq?
refseq
updated 1 day ago by
Ram
44k • written 1 day ago by
curious
▴ 750
0
votes
1
reply
127
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 1 day ago by
jared.andrews07
★ 17k • written 1 day ago by
atan
• 0
0
votes
0
replies
67
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 23 hours ago by
GenoMax
142k • written 23 hours ago by
jway
• 0
0
votes
4
replies
368
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
23 hours ago by
mavy
▴ 10
0
votes
0
replies
84
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 22 hours ago by
Ram
44k • written 23 hours ago by
Christopher
▴ 10
0
votes
3
replies
256
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 21 hours ago by
ATpoint
82k • written 23 hours ago by
shahzaibali
• 0
0
votes
2
replies
169
views
CreateSeuratObject taking very long
seurat
16 hours ago by
eae6d2e7
• 0
0
votes
1
reply
118
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 14 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
adarsh_pp
▴ 40
0
votes
1
reply
101
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 12 hours ago by
Pierre Lindenbaum
162k • written 14 hours ago by
Maksim
• 0
0
votes
0
replies
118
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
12 hours ago by
mtabaka
• 0
0
votes
9
replies
547
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 12 hours ago by
zx8754
11k • written 7 days ago by
hannes.bongartz
• 0
0
votes
3
replies
206
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
11 hours ago by
kmat
• 0
0
votes
0
replies
48
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
11 hours ago by
Emily
▴ 20
0
votes
0
replies
74
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
10 hours ago by
doramora
▴ 10
0
votes
0
replies
40
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
6 hours ago by
irebekah.c
• 0
0
votes
1
reply
88
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 5 hours ago by
Bastien Hervé
5.3k • written 9 hours ago by
bio_info
▴ 10
0
votes
1
reply
296
views
LDhat lookup table
LDhat
updated 4 hours ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
0
replies
29
views
Exon Annotation failed using homer annotatePeaks.pl
homer
alternative-splicing
annotatePeaks
updated 4 hours ago by
Ram
44k • written 5 hours ago by
Alessia
• 0
0
votes
1
reply
2.9k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 4 hours ago by
Ram
44k • written 3.6 years ago by
andemexoax
• 0
0
votes
0
replies
52
views
Can you use a polygenic risk score for a trait (e.g., BMI) in association analyses when it doesn't associate with BMI in the sample it is used?
polygenic-risk-score
imputation
updated 4 hours ago by
Ram
44k • written 8 hours ago by
kl
▴ 10
0
votes
1
reply
165
views
Annotating single cell data automatically
single-cell
updated 4 hours ago by
Ram
44k • written 4 weeks ago by
Gerard
• 0
185 results • Page
2 of 4
Recent Votes
A: Blast - Formatting Output
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
The Biostar Herald for Monday, May 20, 2024
Recent Locations •
All
Brazil,
just now
Chile,
3 minutes ago
United States,
4 minutes ago
United States,
4 minutes ago
New York,
5 minutes ago
Norway,
6 minutes ago
United States,
7 minutes ago
Recent Awards •
All
Popular Question
to
Hamtaro
▴ 50
Popular Question
to
ericrkofman
▴ 20
Scholar
to
chrchang523
10k
Popular Question
to
garcesj
▴ 50
Student
to
Lukas
▴ 50
Scholar
to
Michael
54k
Popular Question
to
octpus616
▴ 100
Recent Replies
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
Comment: Mutation counts corrected by number of samples
by
Ram
44k
> I want to compare the number of mutations This comparison will give you literally no useful information.
Answer: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
Pierre Lindenbaum
162k
something like: seq 1 100 4377380 | while read F ; do wget --no-check-certificate -O - "https://sorfs.ugent.be/database/micrope…
Answer: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
The variability explained by the variables provided to `group.by.vars` is what Harmony will try to remove. Assuming you want to remove the …
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
by
Jeremy Leipzig
22k
That SNP is in an HLA gene which has had a lot of attention and improvement over the years, ranging from kits to software to the reference …
Comment: Overlapping clusters for different biological conditions: Seurat, UMAP
by
Bastien Hervé
5.3k
What is the need of PBMC in your analysis ? If none, removing them from the beginning will allow your clusters to be more specific to your …
Answer: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
I believe `sample_id` are your replicates in either `patient` or `control`. You can do it manually by normalizing the number of cells yo…
Answer: bfctools merge [E::hts_open_format] Failed to open file
by
j.f.akers
• 0
I think the program is trying to open a .vcf.gz.csi file rather than the actual data which is the .vcf.gz file, the csi file is not data, j…
Comment: LDhat lookup table
by
NÚRIA
• 0
Hi! Did you manage to fix this? I run convert successfully on 60 unphased diploid samples (1500bp), hence I used lktable available in LDh…
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
by
F110152169
• 0
It's Parkinson's disease. How do I get the right order?
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
QX
• 0
yes but they did not reply
Traffic: 2200 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6