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42 results • Page
1 of 1
Sort: replies
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Views
Votes
Replies
8
votes
15
replies
725
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 6 hours ago by
GenoMax
141k • written 7 weeks ago by
Sofia
• 0
0
votes
11
replies
456
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
9 hours ago by
atowns21
• 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 17 hours ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 13 hours ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
0
votes
5
replies
282
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 20 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
2
votes
5
replies
259
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
1 hour ago by
Lada
▴ 30
3
votes
4
replies
220
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
14 hours ago by
QX
• 0
2
votes
4
replies
222
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 12 hours ago by
Ram
43k • written 1 day ago by
ashaneev07
▴ 20
3
votes
3
replies
160
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 11 hours ago by
swbarnes2
14k • written 17 hours ago by
M
• 0
0
votes
3
replies
289
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 12 hours ago by
Ram
43k • written 3 days ago by
qudrat.nii
▴ 10
2
votes
3
replies
187
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 22 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
analyst
▴ 30
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 19 hours ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
0
votes
3
replies
125
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 1 hour ago by
Pierre Lindenbaum
161k • written 4 hours ago by
J
• 0
1
vote
2
replies
147
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 16 hours ago by
Bioinfotec
▴ 10 • written 19 hours ago by
starswillfade
▴ 10
0
votes
2
replies
160
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 14 hours ago by
GenoMax
141k • written 21 hours ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
155
views
Highest variable features in single cell data
single-cell
updated 12 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
203
views
Annovar using R package
Annovar
gnomAD
R
12 hours ago by
DKA
▴ 40
0
votes
2
replies
186
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 11 hours ago by
Ram
43k • written 23 hours ago by
Assa Yeroslaviz
★ 1.8k
4
votes
2
replies
364
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 8 hours ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
0
votes
2
replies
163
views
PCA plot
DESeq2
PCAplot
updated 10 minutes ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
1
reply
85
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
updated 10 hours ago by
LauferVA
4.2k • written 11 hours ago by
The_PyPanda
▴ 10
0
votes
1
reply
21
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 20 minutes ago by
Joe
21k • written 51 minutes ago by
sapuizait
▴ 10
0
votes
1
reply
56
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 5 hours ago by
Jeremy Leipzig
22k • written 5 hours ago by
zihanss
• 0
1
vote
1
reply
123
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 12 hours ago by
Ram
43k • written 19 hours ago by
Francesco
▴ 10
0
votes
1
reply
152
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 12 hours ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
0
votes
1
reply
100
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 13 hours ago by
ATpoint
82k • written 13 hours ago by
AaronJaime
• 0
0
votes
1
reply
390
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 18 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
1
reply
57
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 50 minutes ago by
ATpoint
82k • written 4 hours ago by
Aaliya
▴ 10
0
votes
0
replies
32
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
5 hours ago by
turcoa1
• 0
0
votes
0
replies
29
views
RNA-seq: full length gene
identification
gene
full
length
3 hours ago by
Nargis
• 0
0
votes
0
replies
33
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
3 hours ago by
SineWave
• 0
0
votes
0
replies
28
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
2 hours ago by
KABILAN
▴ 40
0
votes
0
replies
81
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
17 hours ago by
Assaf
• 0
0
votes
0
replies
60
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 12 hours ago by
Ram
43k • written 16 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
67
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
16 hours ago by
avocado123
• 0
0
votes
0
replies
109
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 12 hours ago by
Ram
43k • written 1 day ago by
David Langenberger
11k
0
votes
0
replies
54
views
Designing single-stable RNA molecules
structure
RNA
12 hours ago by
Edna
• 0
0
votes
0
replies
63
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
12 hours ago by
simplitia
▴ 130
0
votes
0
replies
57
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
16 hours ago by
Emily
▴ 10
1
vote
0
replies
76
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
16 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
9
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
18 minutes ago by
HarperReed
• 0
0
votes
0
replies
61
views
how to read graph_test output of monocle 3
monocle3
17 hours ago by
synat.keam
▴ 100
42 results • Page
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Recent Votes
How to normalize long-read RNA-seq data for comparison with short-reads
EdgeR analysis with CPM normalzed counts
Alternative splicing convention
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
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Recent Replies
Comment: PCA plot
by
ATpoint
82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
Comment: genome assembly records not present in assembly_summary.txt
by
Joe
21k
If you have the accession numbers can you not use something like `eutils`?
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
ATpoint
82k
For question 1: For question 1: Purpose of indexing a genome/transcriptome/book/anything: https://www.biostars.org/p/212594/ For question …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> using bcftools Show us what you tried
Answer: gvcf joint calling
by
Jeremy Leipzig
22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
Comment: Missing protein (VEGF-A) in String db
by
shalespringer
• 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much, it actually worked!
Answer: Rare Disease Variant Pathway Analysis
by
LauferVA
4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification
by
swbarnes2
14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
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