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681 results • Page
3 of 14
Sort: Views
Rank
Views
Votes
Replies
5
votes
4
replies
725
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
25 days ago by
kirillkirilenko
▴ 40
2
votes
4
replies
720
views
Count all variants from vcf file
variants
vcf
Count
updated 12 days ago by
Pierre Lindenbaum
161k • written 21 months ago by
t.ali
• 0
0
votes
11
replies
719
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
23 days ago by
atowns21
• 0
2
votes
9
replies
711
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 11 days ago by
schmince
• 0
0
votes
1
reply
705
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 18 days ago by
Ram
43k • written 18 days ago by
Dr Huma Naz
• 0
2
votes
11
replies
703
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
2 days ago by
egascon
• 0
3
votes
8
replies
701
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 12 days ago by
Chris Dean
▴ 410 • written 16 days ago by
sovrappensiero
▴ 100
0
votes
3
replies
698
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 10 days ago by
DGTool
▴ 20 • written 22 months ago by
yassine
• 0
0
votes
1
reply
687
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 13 days ago by
GenoMax
142k • written 14 days ago by
tulip
• 0
5
votes
5
replies
673
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 15 days ago by
Mbofire
• 0 • written 24 days ago by
Ming Tommy Tang
★ 3.9k
1
vote
5
replies
672
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 29 days ago by
GenoMax
142k • written 29 days ago by
Luka
• 0
0
votes
7
replies
655
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 16 days ago by
LChart
3.9k • written 19 days ago by
kl
▴ 10
1
vote
5
replies
654
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 25 days ago by
atowns21
• 0 • written 4 months ago by
benjamin.pyenson
• 0
2
votes
5
replies
649
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 28 days ago by
Mensur Dlakic
★ 27k • written 29 days ago by
Giorgio
• 0
3
votes
5
replies
645
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
27 days ago by
n_navy
• 0
0
votes
10
replies
641
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 18 days ago by
i.sudbery
19k • written 26 days ago by
Patadu94
• 0
4
votes
7
replies
639
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
19 days ago by
e.r.zakiev
▴ 210
1
vote
2
replies
630
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 5 hours ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
3
votes
9
replies
629
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 24 days ago by
Istvan Albert
100k • written 26 days ago by
Κοσμάς
• 0
3
votes
8
replies
625
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
12 days ago by
Qroid
▴ 40
0
votes
4
replies
624
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 28 days ago by
ATpoint
82k • written 29 days ago by
rheab1230
▴ 140
0
votes
9
replies
618
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 3 days ago by
Wayne
★ 2.0k • written 12 days ago by
JACKY
▴ 140
1
vote
7
replies
618
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 19 days ago by
bk11
★ 2.5k • written 23 days ago by
starswillfade
▴ 10
1
vote
7
replies
617
views
gvcf joint calling
WES
GATK
VCF
gVCF
21 days ago by
zihanss
• 0
4
votes
7
replies
616
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 24 days ago by
dsull
★ 6.0k • written 25 days ago by
VITALA
• 0
0
votes
1
reply
611
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 17 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
0
votes
0
replies
609
views
Differential accessibility using DiffBinf
diffbind
20 days ago by
Shloka
• 0
5
votes
6
replies
607
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 18 days ago by
me
▴ 760 • written 19 days ago by
Mariana
▴ 40
0
votes
9
replies
605
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
3 days ago by
Arton
▴ 10
7
votes
6
replies
604
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
27 days ago by
analyst
▴ 50
0
votes
1
reply
594
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 3 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
2
votes
5
replies
593
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 6 days ago by
arctic
▴ 40 • written 15 days ago by
M.
▴ 30
0
votes
0
replies
587
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
22 days ago by
biocellbio
• 0
0
votes
3
replies
567
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 9 days ago by
Ram
43k • written 12 weeks ago by
maplewj
▴ 10
0
votes
1
reply
564
views
HOMER on AWS
HOMER
updated 16 days ago by
clairechung112
• 0 • written 2.3 years ago by
Bogdan
★ 1.4k
0
votes
3
replies
564
views
python file for coding potential calculator
cpc2.py
updated 26 days ago by
atharvakarkare14
▴ 40 • written 4 weeks ago by
Ashok
• 0
1
vote
7
replies
561
views
Question regarding WGCNA
WGCNA
Network-construction
9 days ago by
deepak
• 0
1
vote
0
replies
561
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
29 days ago by
mathavanbioinfo
▴ 90
1
vote
8
replies
558
views
Downsampling fastq file
downsample
fastq
18 days ago by
marco.barr
▴ 130
3
votes
3
replies
557
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 29 days ago by
swbarnes2
14k • written 4 weeks ago by
noodle
▴ 580
0
votes
11
replies
552
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
6 days ago by
Tuck898
• 0
0
votes
1
reply
550
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 16 days ago by
Hugo
• 0 • written 5 months ago by
Rachel
• 0
2
votes
5
replies
548
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
20 days ago by
ashaneev07
▴ 20
2
votes
5
replies
546
views
Marking duplicates using UMIs
Deduplication
UMI
updated 26 days ago by
i.sudbery
19k • written 28 days ago by
Lipika
• 0
0
votes
1
reply
542
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 5 days ago by
aw7
▴ 300 • written 29 days ago by
abhishekghadge
• 0
0
votes
8
replies
540
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 18 days ago by
LauferVA
4.2k • written 20 days ago by
jinyu
▴ 10
0
votes
1
reply
537
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 23 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
1
vote
1
reply
531
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
29 days ago by
renan.igor
• 0
3
votes
6
replies
522
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 6 days ago by
Pine
▴ 20 • written 13 days ago by
snajafy
• 0
1
vote
7
replies
511
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
15 days ago by
eebloom
▴ 80
681 results • Page
3 of 14
Recent Votes
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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scideas
▴ 30
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Muhammad
• 0
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▴ 100
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★ 1.8k
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Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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