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44 results • Page
1 of 1
Sort: replies
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8
votes
15
replies
738
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 11 hours ago by
GenoMax
141k • written 7 weeks ago by
Sofia
• 0
0
votes
11
replies
469
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
13 hours ago by
atowns21
• 0
19
votes
10
replies
14k
views
9 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 3 hours ago by
benformatics
3.9k • written 10.8 years ago by
J.F.Jiang
▴ 920
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 21 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 17 hours ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 4 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
2
votes
5
replies
274
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
6 hours ago by
Lada
▴ 30
2
votes
4
replies
230
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 17 hours ago by
Ram
43k • written 1 day ago by
ashaneev07
▴ 20
0
votes
4
replies
178
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
6 minutes ago by
J
• 0
3
votes
4
replies
228
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
18 hours ago by
QX
• 0
1
vote
4
replies
175
views
ScRNA data question
scRNA
Vlnplot
Samples
52 minutes ago by
starswillfade
▴ 10
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 23 hours ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
0
votes
3
replies
297
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 17 hours ago by
Ram
43k • written 3 days ago by
qudrat.nii
▴ 10
3
votes
3
replies
171
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 16 hours ago by
swbarnes2
14k • written 22 hours ago by
M
• 0
2
votes
3
replies
318
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 56 minutes ago by
dsull
★ 5.8k • written 16 days ago by
javanokendo
▴ 60
0
votes
2
replies
211
views
Annovar using R package
Annovar
gnomAD
R
17 hours ago by
DKA
▴ 40
0
votes
2
replies
166
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 19 hours ago by
GenoMax
141k • written 1 day ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
162
views
Highest variable features in single cell data
single-cell
updated 17 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
191
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 16 hours ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
4
votes
2
replies
366
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 13 hours ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
0
votes
2
replies
192
views
PCA plot
DESeq2
PCAplot
updated 4 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
2
replies
132
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
4 hours ago by
The_PyPanda
▴ 10
2
votes
2
replies
130
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 2 hours ago by
dsull
★ 5.8k • written 9 hours ago by
Aaliya
▴ 10
0
votes
2
replies
75
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 hours ago by
GenoMax
141k • written 5 hours ago by
sapuizait
▴ 10
1
vote
1
reply
129
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 17 hours ago by
Ram
43k • written 1 day ago by
Francesco
▴ 10
0
votes
1
reply
106
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 17 hours ago by
ATpoint
82k • written 18 hours ago by
AaronJaime
• 0
0
votes
1
reply
73
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 9 hours ago by
Jeremy Leipzig
22k • written 9 hours ago by
zihanss
• 0
0
votes
1
reply
397
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 22 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
1
reply
162
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 17 hours ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
43
views
RNA-seq: full length gene
identification
gene
full
length
8 hours ago by
Nargis
• 0
0
votes
0
replies
44
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
7 hours ago by
SineWave
• 0
1
vote
0
replies
44
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
7 hours ago by
KABILAN
▴ 50
0
votes
0
replies
72
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
20 hours ago by
avocado123
• 0
0
votes
0
replies
59
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
4 hours ago by
HarperReed
• 0
1
vote
0
replies
80
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
21 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
63
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
21 hours ago by
Emily
▴ 10
0
votes
0
replies
65
views
how to read graph_test output of monocle 3
monocle3
21 hours ago by
synat.keam
▴ 100
2
votes
0
replies
53
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
scRNA
Machinelearning
GenerativeAI
3 hours ago by
Claire Watson
▴ 50
0
votes
0
replies
68
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 17 hours ago by
Ram
43k • written 21 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
112
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 17 hours ago by
Ram
43k • written 1 day ago by
David Langenberger
11k
0
votes
0
replies
88
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
21 hours ago by
Assaf
• 0
0
votes
0
replies
60
views
Designing single-stable RNA molecules
structure
RNA
16 hours ago by
Edna
• 0
0
votes
0
replies
40
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
9 hours ago by
turcoa1
• 0
0
votes
0
replies
68
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
16 hours ago by
simplitia
▴ 130
44 results • Page
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Recent Votes
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
Converting between Ensembl Versions
Comment: what is the purpose of indexing the reference genome (Kallisto)
Answer: what is the purpose of indexing the reference genome (Kallisto)
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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Recent Replies
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis
by
The_PyPanda
▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads
by
Antonio R. Franco
★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
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: 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…
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