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20 results • Page
1 of 1
Sort: Views
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Views
Votes
Replies
0
votes
11
replies
467
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
12 hours ago by
atowns21
• 0
0
votes
1
reply
396
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 21 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
5
replies
286
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
2
replies
208
views
Annovar using R package
Annovar
gnomAD
R
15 hours ago by
DKA
▴ 40
0
votes
2
replies
182
views
PCA plot
DESeq2
PCAplot
updated 3 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
3
replies
166
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 4 hours ago by
Pierre Lindenbaum
161k • written 7 hours ago by
J
• 0
0
votes
2
replies
161
views
Highest variable features in single cell data
single-cell
updated 16 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
1
reply
105
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 16 hours ago by
ATpoint
82k • written 17 hours ago by
AaronJaime
• 0
1
vote
0
replies
79
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
19 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
71
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
19 hours ago by
avocado123
• 0
0
votes
0
replies
67
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
15 hours ago by
simplitia
▴ 130
0
votes
0
replies
64
views
how to read graph_test output of monocle 3
monocle3
20 hours ago by
synat.keam
▴ 100
0
votes
0
replies
62
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
19 hours ago by
Emily
▴ 10
0
votes
2
replies
61
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 43 minutes ago by
GenoMax
141k • written 4 hours ago by
sapuizait
▴ 10
0
votes
0
replies
58
views
Designing single-stable RNA molecules
structure
RNA
15 hours ago by
Edna
• 0
0
votes
0
replies
43
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
6 hours ago by
SineWave
• 0
0
votes
0
replies
43
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
3 hours ago by
HarperReed
• 0
1
vote
0
replies
42
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
5 hours ago by
KABILAN
▴ 50
0
votes
0
replies
40
views
RNA-seq: full length gene
identification
gene
full
length
6 hours ago by
Nargis
• 0
0
votes
0
replies
37
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
8 hours ago by
turcoa1
• 0
20 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: 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…
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…
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