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117,068 results • Page
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0
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0
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13
views
vg autoindex seems stuck after a week of running
vg
pangenome
49 minutes ago by
StevieP
• 0
0
votes
2
replies
62
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
1 hour ago by
kmat
• 0
0
votes
0
replies
30
views
Mapping difference with BWA
variant-calling
samtools
bam
BWA
genomics
2 hours ago by
rj.rezwan
• 0
0
votes
0
replies
31
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
1 minute ago by
Varsha
• 0
0
votes
0
replies
32
views
samtools write-index
samtools
4 hours ago by
LucisTheFather
• 0
0
votes
0
replies
36
views
Kegg Pathways to Circos
Genomics
KEGG
Circos
4 hours ago by
dlera.lozano
▴ 10
0
votes
0
replies
43
views
How to get 2 seurat objects into a DEseq
help
troubleshoot
5 hours ago by
He11oJe11o
• 0
0
votes
0
replies
58
views
DIFFBIND boxplot results, p value not significant
ChIP-seq
DiffBind
9 hours ago by
RD
▴ 10
3
votes
8
replies
253
views
Problem in getting geo file through GEOQUERY
file
download
Geo
8 hours ago by
anasjamshed
▴ 120
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
0
votes
1
reply
125
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 9 hours ago by
andersdetermig
▴ 20 • written 1 day ago by
Christopher
• 0
0
votes
2
replies
150
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
9 hours ago by
ezz3
• 0
1
vote
10
replies
549
views
Add stats to the plot
R
updated 6 hours ago by
GenoMax
142k • written 2 days ago by
Ghada
• 0
0
votes
4
replies
165
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
9 hours ago by
shpak.max
▴ 50
0
votes
2
replies
123
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
updated 11 hours ago by
LChart
3.9k • written 13 hours ago by
Arton
▴ 10
0
votes
1
reply
93
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 10 hours ago by
GenoMax
142k • written 11 hours ago by
s
• 0
0
votes
3
replies
132
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 11 hours ago by
GenoMax
142k • written 11 hours ago by
bioinfo
▴ 150
1
vote
1
reply
81
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
updated 12 hours ago by
GenoMax
142k • written 12 hours 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 14 hours ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
1
vote
3
replies
243
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
4 hours ago by
Pegasus
▴ 100
0
votes
2
replies
151
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
14 hours ago by
Shukai
• 0
1
vote
3
replies
156
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 11 hours ago by
Pierre Lindenbaum
161k • written 15 hours ago by
mrk
• 0
0
votes
3
replies
165
views
z-score of gene set
z-score
scRNA
gene-set
41 minutes ago by
Hien
• 0
2
votes
1
reply
121
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 11 hours ago by
Ram
44k • written 17 hours ago by
ashkan
▴ 160
0
votes
0
replies
71
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 16 hours ago by
GenoMax
142k • written 16 hours ago by
LuciaNhu
• 0
1
vote
2
replies
146
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 14 hours ago by
Ram
44k • written 16 hours ago by
Harshita
• 0
2
votes
0
replies
77
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 12 hours ago by
Ram
44k • written 17 hours ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
85
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 12 hours ago by
Ram
44k • written 17 hours ago by
Fabio Marroni
★ 3.0k
3
votes
5
replies
435
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
17 hours ago by
beantkapoor16
▴ 10
0
votes
1
reply
108
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 17 hours ago by
DBScan
▴ 300 • written 18 hours ago by
brunomiwa
• 0
0
votes
0
replies
68
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
18 hours ago by
Ayda Ecem
• 0
0
votes
3
replies
135
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 12 hours ago by
Ram
44k • written 18 hours ago by
pirku
• 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 12 hours ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
537
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 20 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
72
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
22 hours ago by
Yao
▴ 30
1
vote
1
reply
718
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
19
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
▴ 590
0
votes
0
replies
76
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
1 day ago by
dawnyipingzou
• 0
0
votes
4
replies
208
views
Where to find old version of GATK best practice
gatk
15 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
100
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Peter Chung
▴ 200
0
votes
0
replies
73
views
News:
Online course- Advanced Python for Life Sciences
Python-Programming
Data-Visualisation
Machine-Learning
updated 12 hours ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
114
views
CreateSeuratObject taking very long
seurat
updated 19 hours ago by
Nitin Narwade
★ 1.6k • written 1 day ago by
eae6d2e7
• 0
1
vote
2
replies
187
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
1 day ago by
ojaswinipandey
• 0
0
votes
2
replies
183
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
17 hours ago by
Bjorn
• 0
1
vote
4
replies
280
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
224
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
234
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 1 day ago by
marco.barr
▴ 130 • written 2 days ago by
Mohamed Samir
▴ 20
1
vote
1
reply
116
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
89
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
127
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
1 day ago by
Biostar
2.8k
117,068 results • Page
1 of 2342
Recent Votes
Answer: geom_bar issue in ggplot2 with xlim()
A: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
GO analysis: Different results EnrichGO vs ShinyGO
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
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3.6k
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Recent Replies
Comment: vcf phasing
by
safeassli
▴ 10
Sprry but I'm not an expert in this field. I'm trying to learn Only 0/1, 1/0, and 1/1 genotypes should be phased, as these indicate the pr…
Comment: z-score of gene set
by
Hien
• 0
I have a list of genes in some pathways, I want to see these pathways which are upregulated or downregulated in a total of gene expressions…
Comment: Splitting query fasta file for Diamond Blastp make the process faster?
by
kmat
• 0
Thank you for your quick responce. Sorry for the lack of explanation. Here are some supplementary details regarding the parameters of Diam…
Answer: Splitting query fasta file for Diamond Blastp make the process faster?
by
Mensur Dlakic
★ 27k
There are several pieces of information we are missing here. Did you specify that all 96 threads be used? If so, are all of them being used…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
Yes please see below: TraesCS2B02G372900 TraesCS2B02G375100 TraesCS2B02G374700 TraesCS2B02G382000
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Thanks for your answer, but as far as I know, gProfiler2 does not support bacteria. Could you please suggest alternative websites or softwa…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi Alex, I'm sorry if I wasn't initially clear! The question hasn't changed; I had written in this post that I wanted all pairwise combinat…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
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
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