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44 results • Page
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what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
just now by
Aaliya
▴ 10
0
votes
0
replies
1
view
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
just now by
J
• 0
0
votes
1
reply
17
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 20 minutes ago by
Jeremy Leipzig
22k • written 42 minutes ago by
zihanss
• 0
0
votes
0
replies
10
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
40 minutes ago by
turcoa1
• 0
0
votes
1
reply
69
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
updated 6 hours ago by
LauferVA
4.2k • written 6 hours ago by
The_PyPanda
▴ 10
3
votes
3
replies
144
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 6 hours ago by
swbarnes2
14k • written 13 hours ago by
M
• 0
0
votes
0
replies
46
views
Designing single-stable RNA molecules
structure
RNA
7 hours ago by
Edna
• 0
0
votes
0
replies
55
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
7 hours ago by
simplitia
▴ 130
0
votes
1
reply
83
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 8 hours ago by
ATpoint
82k • written 9 hours ago by
AaronJaime
• 0
0
votes
2
replies
142
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 10 hours ago by
GenoMax
141k • written 17 hours ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
178
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 6 hours ago by
Ram
43k • written 19 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
113
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 8 hours ago by
Ram
43k • written 15 hours ago by
Francesco
▴ 10
1
vote
2
replies
140
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 11 hours ago by
Bioinfotec
▴ 10 • written 14 hours ago by
starswillfade
▴ 10
0
votes
0
replies
59
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
11 hours ago by
avocado123
• 0
0
votes
0
replies
54
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 8 hours ago by
Ram
43k • written 11 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
50
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
11 hours ago by
Emily
▴ 10
1
vote
0
replies
68
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
12 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
56
views
how to read graph_test output of monocle 3
monocle3
12 hours ago by
synat.keam
▴ 100
0
votes
0
replies
74
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
12 hours ago by
Assaf
• 0
0
votes
1
reply
385
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 13 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
208
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
9 hours ago by
QX
• 0
2
votes
1
reply
142
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 19 hours ago by
Adrian Altenhoff
★ 1.1k • written 1 day ago by
hemantcnaik
• 0
0
votes
0
replies
71
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
19 hours ago by
Aspire
▴ 300
2
votes
4
replies
214
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 8 hours ago by
Ram
43k • written 22 hours ago by
ashaneev07
▴ 20
2
votes
3
replies
180
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 17 hours ago by
Pierre Lindenbaum
161k • written 21 hours ago by
analyst
▴ 30
0
votes
1
reply
121
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 21 hours ago by
b.contreras.moreira
▴ 170 • written 22 hours ago by
Broccoli
• 0
0
votes
2
replies
149
views
Highest variable features in single cell data
single-cell
updated 8 hours ago by
Ram
43k • written 21 hours ago by
Kazo
• 0
0
votes
1
reply
148
views
PCA plot
DESeq2
PCAplot
updated 14 hours ago by
jkim
▴ 170 • written 1 day ago by
Aaliya
▴ 10
0
votes
1
reply
139
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 8 hours ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
279
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 8 hours ago by
Ram
43k • written 2 days ago by
qudrat.nii
▴ 10
0
votes
2
replies
189
views
Annovar using R package
Annovar
gnomAD
R
8 hours ago by
DKA
▴ 40
3
votes
8
replies
482
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 23 hours ago by
swbarnes2
14k • written 2 days ago by
Aaliya
▴ 10
1
vote
8
replies
750
views
Adding CB tag to bam file
samtools
bam
updated 20 hours ago by
Pierre Lindenbaum
161k • written 7 days ago by
Maria
• 0
0
votes
5
replies
272
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 15 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
103
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 8 hours ago by
Ram
43k • written 1 day ago by
David Langenberger
11k
4
votes
7
replies
404
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 20 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
0
votes
4
replies
245
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
20 hours ago by
sehriban.buyukkilic
▴ 10
1
vote
2
replies
195
views
alignment result
RNA-seq
samtools
hisat2
22 hours ago by
ahmad.sajad4541
• 0
0
votes
11
replies
445
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
4 hours ago by
atowns21
• 0
8
votes
15
replies
708
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 2 hours ago by
GenoMax
141k • written 7 weeks ago by
Sofia
• 0
4
votes
2
replies
353
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 4 hours ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 14 hours ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 8 hours ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 12 hours ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
44 results • Page
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Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Answer: Missing protein (VEGF-A) in String db
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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.
Comment: Annovar using R package
by
DKA
▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
ATpoint
82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
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