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47 results • Page
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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
19
votes
15
replies
2.3k
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 15 hours ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
0
votes
3
replies
1.7k
views
Running STRUCTURE from command line
STRUCTURE
updated 5 hours ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
2
votes
3
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 7 hours ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
4
votes
10
replies
854
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 18 hours ago by
Alex Reynolds
35k • written 25 days ago by
J
▴ 10
1
vote
1
reply
705
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
4
votes
9
replies
641
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 16 hours ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
1
vote
3
replies
525
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 14 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
1
vote
10
replies
508
views
Add stats to the plot
R
3 hours ago by
Ghada
• 0
3
votes
5
replies
426
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
11 hours ago by
beantkapoor16
▴ 10
3
votes
5
replies
417
views
Super ehancers
enhancers
updated 6 hours ago by
jared.andrews07
★ 17k • written 19 days ago by
Oburah
• 0
1
vote
2
replies
380
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 6 hours ago by
finch
• 0 • written 3 months ago by
star
▴ 10
1
vote
6
replies
358
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
13 hours ago by
Umer
▴ 50
1
vote
4
replies
305
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 5 hours ago by
Ram
44k • written 6 days ago by
Arton
▴ 10
1
vote
4
replies
255
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
3 hours ago by
shpak.max
▴ 50
0
votes
3
replies
237
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 52 minutes ago by
Nyksubuz
▴ 20 • written 5 days ago by
Luqman
• 0
1
vote
2
replies
228
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 16 hours ago by
colindaven
6.4k • written 2 days ago by
Dr.
• 0
1
vote
2
replies
204
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 8 hours ago by
geneontologyhelp
▴ 410 • written 1 day ago by
Pegasus
▴ 100
0
votes
4
replies
197
views
Where to find old version of GATK best practice
gatk
8 hours ago by
Zhenyu Zhang
★ 1.2k
3
votes
8
replies
175
views
Problem in getting geo file through GEOQUERY
file
download
Geo
2 hours ago by
anasjamshed
▴ 120
0
votes
2
replies
172
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
11 hours ago by
Bjorn
• 0
1
vote
3
replies
132
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 4 hours ago by
Pierre Lindenbaum
161k • written 9 hours ago by
mrk
• 0
0
votes
2
replies
131
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
8 hours ago by
Shukai
• 0
0
votes
2
replies
131
views
z-score of gene set
z-score
scRNA
gene-set
updated 8 hours ago by
Ram
44k • written 11 hours ago by
Hien
• 0
1
vote
2
replies
130
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 7 hours ago by
Ram
44k • written 10 hours ago by
Harshita
• 0
0
votes
1
reply
123
views
vcf phasing
beagle
WhatsHap
phasing
updated 13 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
0
votes
3
replies
117
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 5 hours ago by
Ram
44k • written 12 hours ago by
pirku
• 0
0
votes
4
replies
116
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
3 hours ago by
shpak.max
▴ 50
0
votes
3
replies
111
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
bioinfo
▴ 150
0
votes
2
replies
105
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
updated 4 hours ago by
LChart
3.9k • written 6 hours ago by
Arton
▴ 10
0
votes
1
reply
103
views
CreateSeuratObject taking very long
seurat
updated 12 hours ago by
Nitin Narwade
★ 1.6k • written 22 hours ago by
eae6d2e7
• 0
2
votes
1
reply
102
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 4 hours ago by
Ram
44k • written 10 hours ago by
ashkan
▴ 160
0
votes
1
reply
97
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 3 hours ago by
andersdetermig
▴ 20 • written 23 hours ago by
Christopher
• 0
0
votes
1
reply
91
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 17 hours ago by
Pierre Lindenbaum
161k • written 18 hours ago by
Peter Chung
▴ 200
0
votes
2
replies
87
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
2 hours ago by
ezz3
• 0
0
votes
1
reply
87
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 10 hours ago by
DBScan
▴ 300 • written 11 hours ago by
brunomiwa
• 0
0
votes
1
reply
71
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 4 hours ago by
GenoMax
142k • written 5 hours ago by
s
• 0
0
votes
0
replies
65
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
17 hours ago by
dawnyipingzou
• 0
0
votes
0
replies
64
views
News:
Online course- Advanced Python for Life Sciences
Python-Programming
Data-Visualisation
Machine-Learning
updated 5 hours ago by
Ram
44k • written 18 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
64
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 5 hours ago by
Ram
44k • written 10 hours ago by
Fabio Marroni
★ 3.0k
1
vote
1
reply
62
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
4 hours ago by
Tuấn Anh
• 0
2
votes
0
replies
61
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 5 hours ago by
Ram
44k • written 10 hours ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
60
views
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
updated 9 hours ago by
GenoMax
142k • written 10 hours ago by
Christopher
• 0
0
votes
0
replies
59
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
15 hours ago by
Yao
▴ 30
0
votes
0
replies
56
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
12 hours ago by
Ayda Ecem
• 0
0
votes
0
replies
53
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 9 hours ago by
GenoMax
142k • written 10 hours ago by
LuciaNhu
• 0
0
votes
0
replies
32
views
DIFFBIND boxplot results, p value not significant
ChIP-seq
DiffBind
2 hours ago by
RD
▴ 10
47 results • Page
1 of 1
Recent Votes
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
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
Comment: Problem in getting geo file through GEOQUERY
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Recent Replies
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
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 …
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