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705 results • Page
3 of 15
Sort: Views
Rank
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
3
votes
8
replies
737
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
0
votes
11
replies
736
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
25 days ago by
atowns21
• 0
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
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
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 20 days ago by
Dr Huma Naz
• 0
0
votes
1
reply
721
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
696
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
5
votes
5
replies
683
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
7
replies
674
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 18 days ago by
LChart
3.9k • written 22 days ago by
kl
▴ 10
0
votes
9
replies
672
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
1
vote
5
replies
663
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
655
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
646
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
645
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
643
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
634
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 10 hours ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
5
votes
6
replies
633
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
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
ScRNA data question
scRNA
Vlnplot
Samples
updated 22 days ago by
bk11
★ 2.5k • written 26 days ago by
starswillfade
▴ 10
1
vote
7
replies
623
views
gvcf joint calling
WES
GATK
VCF
gVCF
23 days ago by
zihanss
• 0
0
votes
9
replies
617
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
5 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
596
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
1
reply
595
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
0
replies
590
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
24 days ago by
biocellbio
• 0
0
votes
3
replies
588
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 12 days ago by
Ram
44k • written 3 months ago by
maplewj
▴ 10
1
vote
7
replies
584
views
Question regarding WGCNA
WGCNA
Network-construction
12 days ago by
deepak
• 0
0
votes
11
replies
576
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
9 days ago by
Tuck898
• 0
1
vote
8
replies
574
views
Downsampling fastq file
downsample
fastq
21 days ago by
marco.barr
▴ 130
0
votes
3
replies
570
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
560
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
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
8
replies
548
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
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
536
views
RNA seq analysis
DESeq
RNA-seq
6 days ago by
Jacek
▴ 20
3
votes
6
replies
534
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 8 days ago by
Pine
▴ 20 • written 16 days ago by
snajafy
• 0
0
votes
8
replies
533
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 10 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
526
views
cellranger error message
multiplexing
cellranger
updated 11 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
2
votes
5
replies
524
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 6 days ago by
Ram
44k • written 12 days ago by
Prawesh
• 0
1
vote
7
replies
524
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
18 days ago by
eebloom
▴ 80
1
vote
3
replies
520
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 8 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
705 results • Page
3 of 15
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Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
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Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Ram
44k
Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
Comment: Multiplexing for pooled CRISPR screen sequencing
by
GenoMax
142k
> If we switch to pair-end sequencing with dual-index barcode You can use dual-indexing with single end reads. You don't need to do paired…
Comment: Super ehancers
by
jared.andrews07
★ 17k
That is not valid GFF format, so that is probably going to be problematic. See the [GFF spec](https://github.com/The-Sequence-Ontology/Spec…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
finch
• 0
Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
Answer: Is it possible to run CibersortX with a very small number of samples?
by
finch
• 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Ram
44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
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