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Showing top results for tag: ensembl • reset
1
vote
3
replies
81
views
X amino acid in ensembl
aminoacid alignment ensembl protein sequence
updated 5 hours ago by ★ 10k • written 9 hours ago by • 0
4
votes
4
replies
89
views
Which Fasta file and GTF file to use in STAR alignment
STAR ENSEMBL GTF fa
12 hours ago by peru • 0
1
vote
2
replies
165
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 3 days ago by 48k • written 5 days ago by ★ 1.4k
5
votes
3
replies
197
views
Unable to match Ensembl IDs from TCGA-related CNV datasets
Ensembl Number TCGA TCGABiolinks Variation Copy
updated 9 days ago by 72k • written 13 days ago by ▴ 20
10
votes
8
replies
557
views
ENSMUSG number convert to gene name
ensembl gene
updated 20 days ago by 72k • written 22 days ago by ▴ 210
3
votes
4
replies
307
views
How do we handle TPM values after converting from Ensembl to HUGO genes?
ensembl hugo tpm-calculator tpm rna-seq
updated 23 days ago by 87k • written 23 days ago by ★ 1.2k
0
votes
0
replies
87
views
ENSEMBL bigwig RNA-seq tracks for single-gene visual inspection
RNA-Seq tracks bigwig ensembl zebrafish
25 days ago by bernarda • 0
3
votes
3
replies
3.1k
views
Playing With Mysql/Ensembl (I): Mapping 'Gene' To 'Xref'
ensembl mysql
updated 28 days ago by 20 • written 11.0 years ago by 135k
0
votes
3
replies
149
views
Read VEP output from command line in R
vep ensembl R Bash
updated 29 days ago by ▴ 470 • written 29 days ago by ▴ 30
0
votes
2
replies
109
views
Is the ENSEMBL FTP down?
ensembl ftp
29 days ago by liorglic ▴ 340
92
votes
12
replies
38k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 4 weeks ago by • 0 • written 9.2 years ago by ▴ 390
5
votes
8
replies
419
views
Question: Convert Ensembl Transcript Ids Ensmust To Gene Symbol In R
R ENSEMBL gene
updated 11 days ago by 72k • written 4 weeks ago by ▴ 60
1
vote
3
replies
156
views
How to extract the longest CDS from Homo_sapiens.GRCh38.cds.all.fa?
python script biopython ensembl
5 weeks ago by omotosoolatunde01 • 0
2
votes
1
reply
145
views
Ensembl REST to download transcript fastas
ensembl
updated 5 weeks ago by 22k • written 6 weeks ago by • 0
0
votes
1
reply
145
views
Virtual Box of VEP tool for windows
vep virtualbox ensembl Tool
updated 6 weeks ago by 15k • written 6 weeks ago by • 0
2
votes
0
replies
117
views
News: Free Ensembl Browser and REST API virtual workshops in March
Ensembl training REST API workshop genome browser News
updated 6 weeks ago by 99k • written 6 weeks ago by ▴ 90
0
votes
1
reply
92
views
How do I add a GENSCAN track to the Ensembl Gene Summary
Ensembl genscan
updated 6 weeks ago by 22k • written 6 weeks ago by • 0
0
votes
1
reply
99
views
Incomplete MGI to ensembl conversion using Bioc version 3.12
bioMart Ensembl gene conversion R
6 weeks ago by Adriano.Biasini • 0
1
vote
8
replies
662
views
Multiple ensembl gene ID for the same gene name (Symbol), how to deal with this while differential analysis?
RNA-Seq alignment next-gen ensembl
7 weeks ago by Swarna • 0
3
votes
3
replies
3.8k
views
Mapping GRCh38 to ENSEMBL / UCSC ,Gene, transcript , cDNA and Protein IDs and Sequence
RNA-Seq SNP genome Mappping ENSEMBL
updated 7 weeks ago by 20 • written 4.2 years ago by ▴ 110
1
vote
1
reply
147
views
Splice junction coordinates for Ensembl transcripts
Ensembl Splicing Annotation
updated 7 weeks ago by 22k • written 7 weeks ago by • 0
3
votes
7
replies
156
views
Trying to refine REST API query
R ensembl API
updated 8 weeks ago by 22k • written 8 weeks ago by • 0
3
votes
4
replies
167
views
diferentially expressed ensembl ID to gene symbol conversion
DEG Ensembl HGNC_symbol biomart
8 weeks ago by imaparna27 • 0
0
votes
5
replies
160
views
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
ensembl mapping homology
9 weeks ago by nickhir ▴ 30
1
vote
7
replies
186
views
Extract longest transcript from Ensembl gene table
bash gene ensembl R
9 weeks ago by Midge • 0
6
votes
6
replies
289
views
probe ID to ensemble
conversion ensembl probe id
9 weeks ago by dxodnd • 0
4
votes
4
replies
194
views
WTF with the ensembl human genome?
genome ensembl refseq
updated 10 weeks ago by 22k • written 10 weeks ago by ★ 5.3k
5
votes
5
replies
221
views
Why VEP doesn't take strand into account?
vep ensembl snp
updated 10 weeks ago by 22k • written 10 weeks ago by • 0
3
votes
7
replies
190
views
Why VEP annotates non-variants (homozygous reference)?
vep ensembl SNP
updated 10 weeks ago by 22k • written 10 weeks ago by • 0
0
votes
3
replies
176
views
VEP cache issues
software error ensembl vep
updated 11 weeks ago by 22k • written 11 weeks ago by • 0
2
votes
8
replies
222
views
Understanding Variant Effect Predictor results
ensembl vep variant effect predictor
11 weeks ago by caro-ca ▴ 20
0
votes
6
replies
234
views
Unable to find this E coli genome
E coli genome ensembl bacteria download
updated 3 months ago by ★ 10k • written 3 months ago by • 0
6
votes
5
replies
174
views
Is there a package that outputs gene coordinates given a list of Ensembl IDs?
ensembl biopython gene
updated 3 months ago by 48k • written 3 months ago by • 0
2
votes
3
replies
208
views
Does VEP use alternative splicing in their calculations?
VEP Ensembl Variant Effect Predictor
updated 3 months ago by 22k • written 3 months ago by ▴ 20
3
votes
4
replies
199
views
mapping gene type or biotype to ENSEMBL ID
Annotation ensembl Org.Hs.eg.db biomaRt
updated 3 months ago by 5.1k • written 3 months ago by ▴ 10
198
votes
30
replies
112k
views
22 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 • 0 • written 8.1 years ago by 18k
0
votes
1
reply
174
views
Searching a DNA sequence for eukaryotic genes
fasta ensembl dna human chromosome 13
updated 3 months ago by 99k • written 3 months ago by • 0
2
votes
2
replies
307
views
How to how "Gene Legend", "Regulation Legend" & "Human cDNAs" for a DNA sequence
ensembl
3 months ago by mohammad.shoumik.saad.aarman • 0
12
votes
11
replies
2.5k
views
How to deal with the case that one gene symbol matches multiple ensembl ids?
RNA-Seq ensembl
updated 4 months ago by 20 • written 2.4 years ago by ▴ 110
3
votes
3
replies
306
views
Is there any tool/API available to convert GTF/GFF to JSON format?
gtf gff json ncbi ensembl
updated 4 months ago by ★ 2.5k • written 4 months ago by 5.4k
41
votes
6
replies
9.6k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf vcf ensembl tcga somatic Tutorial
4 months ago by Cyriac Kandoth 5.5k
0
votes
3
replies
202
views
How to convert E. coli gene names from biocyc to Ensembl IDs?
ENSEMBL biocyc Escherichia coli conversion R
updated 4 months ago by 20 • written 4 months ago by ★ 3.4k
1
vote
1
reply
213
views
Problem with BiomaRt::useMart function Landscape Genomics
landcape genomics BiomaRt usaMart ensembl plant
updated 4 months ago by 22k • written 4 months ago by ▴ 10
2
votes
4
replies
297
views
Retrieve 5'UTR sequences for ensembl_transcript_id's with unique start/end positions
biomart ensembl R sequence
4 months ago by omit3333 • 0
1
vote
1
reply
161
views
How to find the gene name and classification using Ensembl ID?
genome ensembl lncRNA
updated 5 months ago by 24k • written 5 months ago by ▴ 60
0
votes
0
replies
183
views
How do I get a gtf file to use rnaQUAST
rnaQUAST ensembl gencode gtf gff
5 months ago by kristina.mahan ▴ 130
1
vote
4
replies
239
views
How to get enome feature annotation through NCBI api ?
refseq NCBI ensembl ucsc gene
updated 5 months ago by ★ 2.4k • written 5 months ago by ▴ 40
3
votes
7
replies
425
views
biomaRt error while converting ensembl gene Id to uniprot ID
biomaRt R ensembl uniprot
5 months ago by manaswwm ▴ 130
8
votes
2
replies
723
views
What is the VEP Impact column?
VEP sequencing consequence variant ensembl
written 5 months ago by ▴ 20
2
votes
0
replies
228
views
News: Get Ensembl training, virtually
ensembl training online News
5 months ago by Emily_Ensembl 22k
50 results • Page 1 of 1
Recent Votes
Comment: Genotype Data in PLINK
Comment: Hunting invisible characters?
Comment: Hunting invisible characters?
Comment: A simple tutorial for a complex ComplexHeatmap
Comment: A simple tutorial for a complex ComplexHeatmap
Comment: A simple tutorial for a complex ComplexHeatmap
Answer: Hunting invisible characters?
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Recent Replies
Comment: How can I Extract Transposable element from a new genome assembly? by Philipp Bayer 6.9k
if you can transform the bed to gff (galaxy has tools for that), you could also use liftoff which wraps all of this in a pipeline https://g…
Comment: A simple tutorial for a complex ComplexHeatmap by Rob ▴ 40
Great! Thank you ATpoint
Comment: Hunting invisible characters? by seidel 7.6k
Another way to see hidden characters is to pipe them through octal dump: `cat infile | od -c` this will print out hidden characters, newlin…
Comment: How can I Extract Transposable element from a new genome assembly? by GenoMax 99k
Align your assemblies to each other using an aligner like `lastz` ([**LINK**][1]). You could also use `blat` if you are sure the assemblies…
Comment: Trimmomatic-0.36 not finding adapter directory by GenoMax 99k
It is going to take as long as it takes. You need to be patient and wait until the prompt returns. Based on speed of your CPU/disk things c…
Comment: Hunting invisible characters? by GenoMax 99k
You could have looked at the file using `cat -vet` which would have shown all characters in the file. Printable and non.
Comment: Can't count features with featurecount by avelarbio46 ▴ 10
I'm not sure about three things: What does -M and -O do exactly that could benefit in my case? Why should I specify -t if I don't necessa…
Comment: Hunting invisible characters? by geneticatt ▴ 120
Thank you, using `dos2unix` worked perfectly!
Answer: Hunting invisible characters? by Mensur Dlakic ★ 10k
You may want to read [**this**][1]. I think you may be able to fix your adaper file by typing: dos2unix i5R.txt If an error pops …
Comment: RNA seq analysis; two samples by Ram 32k
Please do not delete posts that have comments/answers.
Comment: ICE normalization using JuicerTools by sckinta ▴ 610
Is there a way to extract ICE bias from balanced .cool file? I know that you can find weight associated with each bin by `cooler dump --bal…
Comment: How to verify putative miRNA by boczniak767 ▴ 740
Yeah, miRNA could be only verified in wet-lab. Take a look at [stem-loop PCR][1]. I've used it and it works really well. [1]: https://j…
Comment: R - A bioinformatic analysis programming language for NGS by Ram 32k
Because this is a plain copy-paste from the novogene page, it has numbers (pointers to specific references that the source has), but not th…
Comment: X amino acid in ensembl by Mensur Dlakic ★ 10k
This is correct. `X` means any amino acid. Most substitution matrices apply identical penalty (`-1`) when any amino-acid is aligned with X …
Answer: differential expression analysis by Mensur Dlakic ★ 10k
I think the numbers you cite are the most extreme values that people will still accept. In most cases I would go for lower p-values (at lea…
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