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711 results • Page
3 of 15
Sort: Views
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Views
Votes
Replies
5
votes
4
replies
742
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
27 days ago by
kirillkirilenko
▴ 40
0
votes
11
replies
739
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
26 days ago by
atowns21
• 0
3
votes
8
replies
738
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 15 days ago by
Chris Dean
▴ 410 • written 19 days ago by
sovrappensiero
▴ 100
2
votes
4
replies
726
views
Count all variants from vcf file
variants
vcf
Count
updated 14 days ago by
Pierre Lindenbaum
161k • written 21 months ago by
t.ali
• 0
0
votes
1
reply
724
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 20 days ago by
Ram
44k • written 21 days ago by
Dr Huma Naz
• 0
1
vote
2
replies
724
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 2 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
0
votes
1
reply
722
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 16 days ago by
GenoMax
142k • written 16 days ago by
tulip
• 0
0
votes
3
replies
707
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 12 days ago by
DGTool
▴ 20 • written 22 months ago by
yassine
• 0
1
vote
1
reply
703
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
5
votes
5
replies
684
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 18 days ago by
Mbofire
• 0 • written 26 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
9
replies
677
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 6 days ago by
Wayne
★ 2.0k • written 15 days ago by
JACKY
▴ 140
0
votes
7
replies
676
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 18 days ago by
LChart
3.9k • written 22 days ago by
kl
▴ 10
1
vote
5
replies
664
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 28 days ago by
atowns21
• 0 • written 4 months ago by
benjamin.pyenson
• 0
0
votes
10
replies
657
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 21 days ago by
i.sudbery
19k • written 29 days ago by
Patadu94
• 0
3
votes
5
replies
653
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
29 days ago by
n_navy
• 0
3
votes
9
replies
648
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 27 days ago by
Istvan Albert
100k • written 29 days ago by
Κοσμάς
• 0
4
votes
7
replies
646
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
22 days ago by
e.r.zakiev
▴ 210
3
votes
8
replies
644
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
15 days ago by
Qroid
▴ 40
4
votes
9
replies
640
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 15 hours ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
5
votes
6
replies
637
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 21 days ago by
me
▴ 760 • written 22 days ago by
Mariana
▴ 40
1
vote
7
replies
628
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 22 days ago by
bk11
★ 2.5k • written 26 days ago by
starswillfade
▴ 10
4
votes
7
replies
627
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 26 days ago by
dsull
★ 6.0k • written 27 days ago by
VITALA
• 0
1
vote
7
replies
625
views
gvcf joint calling
WES
GATK
VCF
gVCF
23 days ago by
zihanss
• 0
0
votes
9
replies
619
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
6 days ago by
Arton
▴ 10
0
votes
1
reply
615
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 19 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
0
votes
0
replies
613
views
Differential accessibility using DiffBinf
diffbind
22 days ago by
Shloka
• 0
2
votes
5
replies
609
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 9 days ago by
arctic
▴ 40 • written 18 days ago by
M.
▴ 30
0
votes
1
reply
600
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
0
votes
1
reply
598
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 5 days ago by
valdirbarth
▴ 20 • written 13 months ago by
Salomé
• 0
0
votes
3
replies
592
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 12 days ago by
Ram
44k • written 3 months ago by
maplewj
▴ 10
0
votes
0
replies
590
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
25 days ago by
biocellbio
• 0
1
vote
7
replies
585
views
Question regarding WGCNA
WGCNA
Network-construction
12 days ago by
deepak
• 0
1
vote
8
replies
578
views
Downsampling fastq file
downsample
fastq
21 days ago by
marco.barr
▴ 130
0
votes
11
replies
578
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
9 days ago by
Tuck898
• 0
0
votes
3
replies
571
views
python file for coding potential calculator
cpc2.py
updated 28 days ago by
atharvakarkare14
▴ 40 • written 4 weeks ago by
Ashok
• 0
0
votes
1
reply
566
views
HOMER on AWS
HOMER
updated 18 days ago by
clairechung112
• 0 • written 2.3 years ago by
Bogdan
★ 1.4k
2
votes
5
replies
562
views
Marking duplicates using UMIs
Deduplication
UMI
updated 29 days ago by
i.sudbery
19k • written 4 weeks ago by
Lipika
• 0
0
votes
1
reply
559
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 19 days ago by
Hugo
• 0 • written 5 months ago by
Rachel
• 0
2
votes
5
replies
556
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
23 days ago by
ashaneev07
▴ 20
0
votes
8
replies
550
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 21 days ago by
LauferVA
4.2k • written 23 days ago by
jinyu
▴ 10
0
votes
1
reply
550
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 8 days ago by
aw7
▴ 300 • written 4 weeks ago by
abhishekghadge
• 0
0
votes
1
reply
544
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 26 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
5
votes
7
replies
540
views
RNA seq analysis
DESeq
RNA-seq
6 days ago by
Jacek
▴ 20
3
votes
6
replies
537
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 9 days ago by
Pine
▴ 20 • written 16 days ago by
snajafy
• 0
0
votes
8
replies
534
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 2 days ago by
Pierre Lindenbaum
161k • written 11 days ago by
ajbarrett98
• 0
1
vote
5
replies
530
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
28 days ago by
anasjamshed
▴ 120
1
vote
4
replies
528
views
cellranger error message
multiplexing
cellranger
updated 11 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
1
vote
7
replies
525
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
18 days ago by
eebloom
▴ 80
2
votes
5
replies
524
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 7 days ago by
Ram
44k • written 13 days ago by
Prawesh
• 0
1
vote
3
replies
524
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 13 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
711 results • Page
3 of 15
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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