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117,063 results • Page
1 of 2342
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0
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0
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5
views
DIFFBIND boxplot results, p value not significant
ChIP-seq
DiffBind
2 minutes ago by
DINESHR
▴ 10
1
vote
5
replies
60
views
Problem in getting geo file through GEOQUERY
file
download
Geo
updated just now by
ATpoint
82k • written 1 hour ago by
anasjamshed
▴ 120
0
votes
1
reply
75
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 20 minutes ago by
andersdetermig
▴ 20 • written 20 hours ago by
Christopher
• 0
0
votes
2
replies
36
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
16 minutes ago by
ezz3
• 0
1
vote
10
replies
473
views
Add stats to the plot
R
41 minutes ago by
Ghada
• 0
0
votes
4
replies
59
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
35 minutes ago by
shpak.max
▴ 50
0
votes
2
replies
76
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
updated 1 hour ago by
LChart
3.9k • written 3 hours ago by
Arton
▴ 10
0
votes
1
reply
43
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 1 hour ago by
GenoMax
142k • written 2 hours ago by
s
• 0
0
votes
3
replies
77
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 2 hours ago by
GenoMax
142k • written 2 hours ago by
bioinfo
▴ 150
799
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
1
vote
1
reply
51
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
1 hour ago by
Tuấn Anh
• 0
2
votes
3
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 4 hours ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
1
vote
2
replies
194
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 5 hours ago by
geneontologyhelp
▴ 410 • written 1 day ago by
Pegasus
▴ 100
0
votes
2
replies
126
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
5 hours ago by
Shukai
• 0
1
vote
3
replies
109
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 2 hours ago by
Pierre Lindenbaum
161k • written 6 hours ago by
mrk
• 0
0
votes
2
replies
124
views
z-score of gene set
z-score
scRNA
gene-set
updated 5 hours ago by
Ram
44k • written 8 hours ago by
Hien
• 0
2
votes
1
reply
95
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 2 hours ago by
Ram
44k • written 8 hours ago by
ashkan
▴ 160
0
votes
0
replies
49
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 7 hours ago by
GenoMax
142k • written 7 hours ago by
LuciaNhu
• 0
1
vote
2
replies
123
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 4 hours ago by
Ram
44k • written 7 hours ago by
Harshita
• 0
2
votes
0
replies
55
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 3 hours ago by
Ram
44k • written 7 hours ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
59
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 3 hours ago by
Ram
44k • written 7 hours ago by
Fabio Marroni
★ 3.0k
0
votes
0
replies
55
views
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
updated 7 hours ago by
GenoMax
142k • written 8 hours ago by
Christopher
• 0
3
votes
5
replies
422
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
8 hours ago by
beantkapoor16
▴ 10
0
votes
1
reply
84
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 8 hours ago by
DBScan
▴ 300 • written 9 hours ago by
brunomiwa
• 0
0
votes
0
replies
53
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
9 hours ago by
Ayda Ecem
• 0
0
votes
3
replies
113
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 3 hours ago by
Ram
44k • written 9 hours ago by
pirku
• 0
0
votes
3
replies
1.7k
views
Running STRUCTURE from command line
STRUCTURE
updated 3 hours ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
523
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 11 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
56
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
12 hours ago by
Yao
▴ 30
1
vote
1
reply
700
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
17
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 580
0
votes
0
replies
62
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
14 hours ago by
dawnyipingzou
• 0
0
votes
4
replies
187
views
Where to find old version of GATK best practice
gatk
5 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
88
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 15 hours ago by
Pierre Lindenbaum
161k • written 15 hours ago by
Peter Chung
▴ 200
0
votes
0
replies
60
views
News:
Online course- Advanced Python for Life Sciences
Python-Programming
Data-Visualisation
Machine-Learning
updated 3 hours ago by
Ram
44k • written 16 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
100
views
CreateSeuratObject taking very long
seurat
updated 9 hours ago by
Nitin Narwade
★ 1.6k • written 19 hours ago by
eae6d2e7
• 0
1
vote
2
replies
174
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
1 day ago by
ojaswinipandey
• 0
0
votes
2
replies
168
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
8 hours ago by
Bjorn
• 0
1
vote
4
replies
265
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 1 day ago by
Ram
44k • written 1 day ago by
Harshita
• 0
2
votes
4
replies
208
views
Filter Genome for Specific Sites
bedtools
updated 1 day ago by
Ram
44k • written 1 day ago by
Anita
• 0
0
votes
3
replies
223
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 1 day ago by
marco.barr
▴ 130 • written 1 day ago by
Mohamed Samir
▴ 20
1
vote
1
reply
103
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
niruf
• 0
0
votes
0
replies
77
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 1 day ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
112
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
1 day ago by
Biostar
2.8k
3
votes
5
replies
408
views
Super ehancers
enhancers
updated 3 hours ago by
jared.andrews07
★ 17k • written 19 days ago by
Oburah
• 0
0
votes
1
reply
119
views
vcf phasing
beagle
WhatsHap
phasing
updated 10 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
0
votes
2
replies
188
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
1 day ago by
sainavyav22
• 0
0
votes
1
reply
598
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 1 day ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
172
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 1 day ago by
Ram
44k • written 1 day ago by
Sony
▴ 10
0
votes
3
replies
185
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 1 day ago by
Ram
44k • written 1 day ago by
Bioinformatics_begginner
▴ 20
117,063 results • Page
1 of 2342
Recent Votes
Comment: Problem in getting geo file through GEOQUERY
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
Comment: Why does assigning genes with biomart give me different values than using a tran
Comment: Multiplexing for pooled CRISPR screen sequencing
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
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Recent Replies
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
• 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",comparis…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
by
bk11
★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
Dave Carlson
★ 1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
I want to get lot of files through code
Comment: Problem in getting geo file through GEOQUERY
by
GenoMax
142k
Query seems to be timing out. Try getting the file directly here: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1145/matrix/GSE1145-GP…
Comment: Add stats to the plot
by
Ghada
• 0
Thanks for the help. Unfortunately, did not work :( error in asserttat_group_columns_exists(data) : data should contain group1 and grou…
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
How about following https://www.ebi.ac.uk/chembl/web_components/explore/activities/ --> Select a compound --> Related Targets button --> D…
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