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Showing top results for tag: ensembl • reset
1
vote
0
replies
61
views
Tool: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart annotation Ensembl
2 days ago by Shred ▴ 380
3
votes
2
replies
261
views
BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene symbols?
ensembl BioMart
updated 5 days ago by ▴ 220 • written 5 days ago by ▴ 30
2
votes
1
reply
96
views
command line VEP and VEP web interface return different results.
ensembl vep
updated 6 days ago by 22k • written 6 days ago by ▴ 60
1
vote
2
replies
156
views
retrieving entire genomic sequence contents of a database
genomes mining database ftp ensembl
updated 7 days ago by ★ 1.7k • written 11 days ago by • 0
1
vote
1
reply
140
views
ChEMBL ID to Ensembl ID
ChEMBL Ensembl
updated 8 days ago by ▴ 390 • written 9 days ago by ★ 8.7k
2
votes
3
replies
159
views
Contigs and scaffold in reference genome
BWA Ensembl Genome Reference HiSat NCBI
updated 13 days ago by 104k • written 13 days ago by ▴ 370
1
vote
8
replies
277
views
biomaRt: Timeout on getBM().
biomart ensembl
updated 13 days ago by 22k • written 13 days ago by • 0
1
vote
1
reply
130
views
RS numbers and "novelty"
biomaRt WGS ensembl SNP
updated 18 days ago by 22k • written 18 days ago by • 0
2
votes
2
replies
196
views
Is there a way to bulk download orthologue pairwise alignment data from ensembl?
alignment orthologue pairwise ensembl
18 days ago by theo • 0
3
votes
6
replies
325
views
Ensembl encoding problem
gz encoding file Ensembl
updated 18 days ago by 22k • written 18 days ago by • 0
0
votes
7
replies
300
views
Ensembl Highlighted Exons Don't Match Coordinates
ensembl
updated 28 days ago by 22k • written 28 days ago by ▴ 610
0
votes
4
replies
239
views
biomaRt does not convert entrez gene id to ensembl gene id
biomaRt ensembl entrez NCBI
updated 28 days ago by 104k • written 28 days ago by • 0
2
votes
3
replies
149
views
Retrieving the corresponding Haplotype CDS from Ensembl
gene Ensembl protein Haplotype
updated 4 weeks ago by 22k • written 4 weeks ago by ★ 2.9k
3
votes
6
replies
335
views
VEP chromosome name query
ensembl VCF annotation VEP
5 weeks ago by prasundutta87 ▴ 570
2
votes
1
reply
185
views
Error: unexpected symbol using BiomaRt in R
ensembl r biomart biomaRt R
updated 5 weeks ago by 75k • written 5 weeks ago by • 0
0
votes
4
replies
236
views
PRIDE ENSEMBL
ensembl peptides pride
5 weeks ago by desptsp • 0
3
votes
1
reply
133
views
canonical transcript from vep
ensembl transcript appris canonical tsl
updated 6 weeks ago by 22k • written 6 weeks ago by ▴ 90
4
votes
3
replies
198
views
Convert UCSC isoform ID to Ensembl transcript ID
Rna-seq Ensembl Genomics assembly UCSC
updated 5 weeks ago by ★ 1.4k • written 6 weeks ago by • 0
3
votes
6
replies
334
views
Is Ensembl VEP down right now?
Ensembl VEP
updated 8 weeks ago by ▴ 260 • written 8 weeks ago by ▴ 140
2
votes
5
replies
2.4k
views
Unable to access ensembl biomart archives via R
R ensembl biomart
updated 8 weeks ago by ▴ 10 • written 23 months ago by • 0
0
votes
2
replies
185
views
How can I retrieve genomic sequences from ENSEMBL in a window both up stream and downstream of the TSS?
sequence Genome ensembl motif
updated 9 weeks ago by 22k • written 9 weeks ago by • 0
2
votes
14
replies
511
views
Extract information from Ensembl
SNP automation python Ensembl
updated 8 weeks ago by 49k • written 9 weeks ago by • 0
1
vote
0
replies
238
views
Ensembl Homology: Human orthologs of mouse genes labled "many2many" but correspond to a single mouse ortholog
homology Ensembl
9 weeks ago by adam.faranda ▴ 90
3
votes
1
reply
135
views
VEP Disk Space
VEP Ensembl
updated 10 weeks ago by 22k • written 10 weeks ago by ▴ 40
0
votes
2
replies
203
views
Find all genes in multiple regions
ucsc ensembl biomart
updated 10 weeks ago by 13k • written 10 weeks ago by • 0
7
votes
9
replies
7.2k
views
7 follow
Fasta file and GTF file for STAR alignment
STAR ensembl
updated 11 weeks ago by 52k • written 3.2 years ago by ▴ 50
11
votes
7
replies
434
views
Why is human genome FASTA file on GENCODE much smaller than that on ENSEMBL?
reference genome GENCODE ENSEMBL
updated 9 weeks ago by 104k • written 11 weeks ago by ▴ 60
2
votes
5
replies
304
views
VEP, dbNSFP, Offline Mode, Cache version
Annotation VEP dbNSFP Ensembl
updated 11 weeks ago by 22k • written 11 weeks ago by • 0
2
votes
4
replies
324
views
20,000 Ensembl gene IDs with external gene name in hg19 but not in hg38
ensembl biomart
11 weeks ago by loughrae ▴ 70
4
votes
4
replies
384
views
Obtaining variant allele frequencies with the Ensembl API
perl Ensembl API variant frequency
updated 11 weeks ago by 22k • written 12 weeks ago by ▴ 80
1
vote
5
replies
346
views
switch off warning in blast command line
efetch ensembl warnings
updated 12 weeks ago by ★ 12k • written 12 weeks ago by ▴ 570
2
votes
1
reply
163
views
IGH on Ensembl
Ensembl IGH
updated 12 weeks ago by 22k • written 12 weeks ago by ▴ 20
0
votes
1
reply
126
views
Export ensembl efetch in comma-delimited format
format efetch ensembl
updated 12 weeks ago by 104k • written 12 weeks ago by ▴ 570
27
votes
12
replies
18k
views
9 follow
What is a gene transcript?
sequencing ensembl gene transcript
updated 12 weeks ago by • 0 • written 4.3 years ago by ▴ 40
0
votes
4
replies
256
views
biomart returns several ensembl ids for one gene
scrna-seq ensembl biomart r
12 weeks ago by fifty_fifty ▴ 10
0
votes
0
replies
132
views
How to extract ancestral sequence for Cow from 46 eutherian mammals EPO Ensembl?
Ensembl sequences EPO Ancestral
12 weeks ago by Claire • 0
2
votes
3
replies
243
views
Using VEP custom on ClinVar error - Couldn't find index.
vep custom ensembl clinvar
12 weeks ago by milwaukee • 0
1
vote
2
replies
137
views
Ensembl fasta DNA data
ensembl genome mitochondria
3 months ago by kt_b_93 ▴ 10
4
votes
3
replies
274
views
Liftover vs Ensembl Crossmap
crossmap liftover converter assembly ensembl
12 weeks ago by Thind amarinder ▴ 180
8
votes
3
replies
325
views
BioMart servers down again...
ensembl biomart
3 months ago by Tai ▴ 10
0
votes
0
replies
113
views
Does PRIDE have peptides from nr, RefSeq, or ensembl lnRNAs?
PRIDE ensembl peptides seq ref
updated 3 months ago by 8.2k • written 3 months ago by • 0
0
votes
3
replies
216
views
Where can I find a complete mapping of Gencode versions to Ensembl versions?
gene-id gencode ensembl gene
updated 12 weeks ago by 104k • written 3 months ago by • 0
205
votes
31
replies
115k
views
24 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 3 months ago by ▴ 200 • written 8.4 years ago by 19k
2
votes
3
replies
295
views
X amino acid in ensembl
aminoacid alignment ensembl protein sequence
updated 3 months ago by ★ 12k • written 3 months ago by • 0
5
votes
5
replies
637
views
Which Fasta file and GTF file to use in STAR alignment
STAR ENSEMBL GTF fa
updated 3 months ago by ▴ 120 • written 3 months ago by • 0
1
vote
2
replies
328
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 3 months ago by 52k • written 3 months ago by ★ 1.4k
1
vote
2
replies
1.2k
views
Convert multiple rows value retrieved from ensemble biomart to comma separated list for a common ensemble gene ID.
ensembl Biomart R geneontology
updated 5 weeks ago by 34k • written 3 months ago by • 0
5
votes
3
replies
408
views
Unable to match Ensembl IDs from TCGA-related CNV datasets
Ensembl Number TCGA TCGABiolinks Variation Copy
updated 3 months ago by 75k • written 3 months ago by ▴ 20
10
votes
8
replies
1.2k
views
ENSMUSG number convert to gene name
ensembl gene
updated 4 months ago by 75k • written 4 months ago by ▴ 210
3
votes
4
replies
457
views
How do we handle TPM values after converting from Ensembl to HUGO genes?
ensembl hugo tpm-calculator tpm rna-seq
updated 4 months ago by 88k • written 4 months ago by ★ 1.2k
50 results • Page 1 of 1
Recent Votes
Enhanced Volcano removal of labels
A: Enhanced Volcano removal of labels
Answer: What does that dip in the density plot mean from a single cell data analysis?
Comment: What does that dip in the density plot mean from a single cell data analysis?
Answer: What does that dip in the density plot mean from a single cell data analysis?
Answer: Which method is the best for using in "dba.count" in Diffbind R package
Answer: Which method is the best for using in "dba.count" in Diffbind R package
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Recent Replies
Comment: use a list of id to extract sequence from different genomics by LZH289 • 0
thank you!
Comment: What does betaPrior do in DESEQ? by i.sudbery 12k
Those DE genes - is that after a log fold change cut off?
Comment: How to filter VEP results of "missing values" by Yiming • 0
Thank you so much! I found an error with my code. And this works: filter_vep -i VEP_annotated.vcf -o VEP_filtered.vcf --format vcf --fo…
Comment: use a list of id to extract sequence from different genomics by GenoMax 104k
Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. <br /> <img src="…
Comment: gnomaAD exome and genome AF differences by humzakhan340 • 0
The point that genomes are much larger and more computationally intensive to work with is well-taken. However, promoter information is not…
Comment: ERROR [mem_sam_pe] paired reads have different names -- during binning in metaW by swbarnes2 10k
Do you understand what the problem is? Have you figured out which step introduced it?
Comment: gene expression of specifics gene by Bioinformatics1 • 0
Thanks Hyper-Odin
Comment: inquiry related to snpsift by rheab1230 • 0
I have one question related to earlier step where you are formating the .vcf file. You are removing white space and removing format tags ex…
Comment: inquiry related to snpsift by rheab1230 • 0
Hey Kevin, its working now. Earlier I use conda to install the software. But that is not working. So I went to bcftools site and downloaded…
Comment: What does that dip in the density plot mean from a single cell data analysis? by m.sadman.sakib ▴ 100
Thank you very much for the great explanation! Really appreciate it!
Comment: Which method is the best for using in "dba.count" in Diffbind R package by m.sadman.sakib ▴ 100
Thank you very much, Rory!
Comment: How to merge folders that have similar (not the same) names, in a folder keeping by cpad0112 16k
**Before** ``` $ tree . . ├── 123_S1_R1_001 │   └── 123_S1_R1_001.fastq.gz ├── 123_S1_R2_001 │   └── 123_S1_R2_001.fastq.gz ├── 456_S25_R1…
Comment: SNP density plot of aedes genome using bed file by Hamid Ghaedi ★ 1.7k
There is no figure to look at that!
Comment: How to filter VEP results of "missing values" by GenoMax 104k
Looking at the [examples of filters on this page][1] something to try `--filter "LoF_filter not exists"`or `--filter "not LoF_filter`? …
Answer: Measuring pairwise distances between residues/atoms in structural alignment of p by Woa ★ 2.8k
haven't used Pymol for a while but I think you can write a script to automate the analysis rather than doing interactively
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