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1,413 results • Page
1 of 29
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Filtering for tag:
annotation
•
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0
votes
1
reply
28
views
Is it possible to annotate a file for the human genome using the command line without using an amino acid sequence
Annotation
human
DNA
PROVEAN
updated 16 minutes ago by
GenoMax
99k • written 1 hour ago by
kamanovae
• 0
0
votes
0
replies
10
views
braker2 output
braker2
braker
annotation
genome
just now by
praasu
▴ 30
2
votes
6
replies
296
views
Generate a file with SNPs given a WGS dataset
annotation
snp
ngs
1 day ago by
iibrams07
• 0
2
votes
9
replies
173
views
Converting Braker2 gtf output to gff then genbank
annotation
38 minutes ago by
robert.murphy
▴ 40
2
votes
3
replies
159
views
How are transcriptome annotations published?
RNAseq
annotation
publish
transcriptome
2 days ago by
Dunois
▴ 620
0
votes
0
replies
38
views
How can I add text label outside the tree in iTOL ?
iTOL
annotation
tree
label
4 days ago by
anran04100
• 0
0
votes
4
replies
209
views
SnpEff not correctly annotating multiple-nucleotide polymorphisms
annotation
snpEff
4 days ago by
Thoth
• 0
0
votes
2
replies
567
views
Maker Failed while doing repeat masking
maker
annotation
RepBase
RepeatMasker
updated 7 days ago by
lieven.sterck
10k • written 11 months ago by
jamie.pike
▴ 60
3
votes
7
replies
427
views
7 follow
Annotation of non model fish (mahi mahi) genome
Assembly
Annotation
updated 7 days ago by
Juke34
★ 5.3k • written 9 months ago by
kspata
▴ 70
3
votes
7
replies
239
views
How to add gene function/protein name, start and end position to DESeq2 results for bacteria
deseq2
annotation
updated 10 days ago by
Michael Dondrup
48k • written 10 days ago by
Miguel
• 0
0
votes
1
reply
85
views
MSI cslculation
bed
sequencing
annotation
updated 12 days ago by
German.M.Demidov
★ 2.0k • written 12 days ago by
berk.gonenc
• 0
0
votes
0
replies
61
views
How to covert VCF-like to ICGC-like vcf Format
conversion
annotation
12 days ago by
ekwame
▴ 70
1
vote
5
replies
273
views
SingleR Cluster-wise annotation
Seurat
SingleR
annotation
scRNA-seq
CellType
updated 12 days ago by
Kevin Blighe
72k • written 14 days ago by
mvis1231
▴ 60
0
votes
1
reply
168
views
2 transcript_id values for the same tRNA in GTF file
GTF
arabidopsisthaliana
annotation
updated 16 days ago by
Santosh Anand
5.3k • written 17 days ago by
hashkolnikov
• 0
6
votes
9
replies
508
views
Choosing a single consensus promoter/transcript for each gene (Mouse)
annotation
ucsc
general
updated 15 days ago by
GenoMax
99k • written 17 days ago by
srhic
▴ 40
0
votes
0
replies
60
views
Stringtie output shows no expression for reference genes
stringtie
programming
annotation
transcriptome
rna
17 days ago by
samhairle
• 0
8
votes
3
replies
212
views
Is there any gene nomenclature conversion tool that recognizes old names?
genomics
R
annotation
updated 17 days ago by
patelk26
▴ 230 • written 17 days ago by
emibaffo
▴ 20
1
vote
1
reply
177
views
Understanding blast2go annotation result
combinedGOgraph
annotation
blast2go
updated 18 days ago by
Istvan Albert
87k • written 18 days ago by
kmkdesilva
▴ 90
8
votes
6
replies
442
views
Translating gene names to entrez id's
database
annotation
biopython
gene
python
18 days ago by
Julian
• 0
1
vote
2
replies
191
views
I need to retrieve the genomic locations of all genes in the given read count matrix
RNAseq
annotation
TEffectR
r
19 days ago by
pavelasquezv
▴ 10
2
votes
3
replies
361
views
featureCounts - ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file
genome
annotation
database
alignment
updated 19 days ago by
cpad0112
15k • written 19 days ago by
pavelasquezv
▴ 10
2
votes
3
replies
294
views
search of genomic annotation databases
genomics
annotation
20 days ago by
ouchenerima571
• 0
2
votes
4
replies
266
views
GTF format feature definitions
annotation
updated 20 days ago by
i.sudbery
11k • written 20 days ago by
robert.murphy
▴ 40
0
votes
0
replies
84
views
Best way for finding annotated counterparts of unknown transcript after BLAST
blast
efetch
pipeline
annotation
21 days ago by
Mathias
• 0
0
votes
0
replies
81
views
Unable to get root element from XML file
blast
galaxy
annotation
21 days ago by
Pamela
• 0
0
votes
0
replies
84
views
Should one keep softmasking when combining gff+fasta to gbk format?
annotation
25 days ago by
robert.murphy
▴ 40
0
votes
1
reply
1.9k
views
No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package
ChIP-Seq
annotation
updated 25 days ago by
hukai916
• 0 • written 5.5 years ago by
MarcinKosinski
▴ 10
0
votes
0
replies
71
views
Augustus training with partial transcriptome?
augustus
maker
maker2
annotation
26 days ago by
DNAlias
▴ 10
4
votes
3
replies
187
views
How to get a mapping between KEGG module and KEGG orthologs?
KEGG
Annotation
Ortholog
Module
updated 26 days ago by
Elucidata
▴ 240 • written 28 days ago by
O.rka
▴ 290
0
votes
7
replies
332
views
Different gen identifiers with the same gene name [HTA 2.0 microarrays]
HTA2.0
annotation
microarrays
updated 29 days ago by
zhouv2017
• 0 • written 6 months ago by
Hamtaro
▴ 10
7
votes
5
replies
1.6k
views
Tool:
AGAT - Another Gff/Gtf Analysis Toolkit
annotation
gff
gtf
toolkit
Tool
29 days ago by
Juke34
★ 5.3k
0
votes
2
replies
120
views
Interpreting first round of maker
maker
busco
annotation
updated 4 weeks ago by
Dave Carlson
▴ 610 • written 4 weeks ago by
gilsorek12
• 0
0
votes
0
replies
107
views
Using InterProScan - ATPase results only
sequence
InterProScan
annotation
4 weeks ago by
damt09
• 0
0
votes
0
replies
88
views
Using Maker to map foward annotations from reference gff
annotation
4 weeks ago by
robert.murphy
▴ 40
1
vote
2
replies
102
views
How to annotate unclassified proteins?
annotation
updated 5 weeks ago by
Mensur Dlakic
★ 10k • written 5 weeks ago by
BiomedicalTissueIng
▴ 20
0
votes
2
replies
88
views
Modifying an annotation files after transgene insertion
transgene
insertion
gtf
annotation
5 weeks ago by
Assa Yeroslaviz
★ 1.5k
1
vote
3
replies
99
views
how to annotate Circular RNA gene type?
RNA-Seq
Circular RNA
annotation
5 weeks ago by
modarzi
▴ 140
0
votes
3
replies
99
views
Can you use high quallity annotation of very closely related to annotation novel genome
annotation
5 weeks ago by
robert.murphy
▴ 40
0
votes
0
replies
90
views
Advantages of different methods to transfer GO annotations
RNA-Seq
GO
Annotation
5 weeks ago by
Rogerio Ribeiro
▴ 50
2
votes
3
replies
162
views
VEP is very slow. Fork doesnt seem to work
vep
annotation
updated 6 weeks ago by
Emily_Ensembl
22k • written 6 weeks ago by
nickhir
▴ 30
0
votes
0
replies
95
views
How to download output files from PANNZER2 web server?
Annotation
6 weeks ago by
nazninislamnif
▴ 20
4
votes
5
replies
282
views
How to select a "representative" transcript in multiple transcript variants from annotation with ANNOVAR and gencode
annovar
gencode
transcript
SNP
annotation
6 weeks ago by
svlachavas
▴ 730
3
votes
5
replies
168
views
Nitrogen fixing enzyme annotation with HMMER and DIAMOND?
annotation
genome
metagenome
updated 6 weeks ago by
Michael Dondrup
48k • written 6 weeks ago by
robert.murphy
▴ 40
0
votes
0
replies
106
views
Why does KAAS use SBH for partial genomes?
orthology
blast
reciprocal best hit
annotation
6 weeks ago by
Dunois
▴ 620
0
votes
2
replies
125
views
minimap2 alignment for maker
maker
minimap2
annotation
alignment
7 weeks ago by
gilsorek12
• 0
1
vote
1
reply
143
views
Splice junction coordinates for Ensembl transcripts
Ensembl
Splicing
Annotation
updated 7 weeks ago by
Emily_Ensembl
22k • written 7 weeks ago by
AJ_S
• 0
2
votes
2
replies
117
views
COG database download error (part-1)
cog
annotation
ftp
updated 7 weeks ago by
Mensur Dlakic
★ 10k • written 7 weeks ago by
Shaminur
▴ 160
2
votes
7
replies
426
views
Annotate hs37d5 genome calls using VEP
vep
annotation
1kgenomes
hs37d5
written 9 months ago by
igor
• 0
2
votes
2
replies
142
views
Maker Annotation - multiple gene models give same blastp match
genome
annotation
Maker
updated 8 weeks ago by
lieven.sterck
10k • written 8 weeks ago by
MH85
• 0
10
votes
18
replies
772
views
Redirecting pHMMER output to /dev/null
annotation
protein
HMMER
gene
genome
updated 8 weeks ago by
bashir
• 0 • written 2.0 years ago by
mss
▴ 40
1,413 results • Page
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Recent Votes
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Comment: What to put in my Github
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OP has said that they are a PhD student but if they are working on an industry sponsored project then only way to show programming proficie…
Comment: correlation analysis of a single variable versus multiple variables
by
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My gene of interest has been implicated in opposing functions. In some types of cancer, it is claimed to be protective, in others it seems …
Comment: Database/list of disease complications
by
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99k
See: https://www.biostars.org/p/492845/
Comment: How to get GO terms to specific to perticular biological process
by
BISEP
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@geneticatt I can get all bioloical process category not able to get to specific biological process like development I want to select only…
Comment: What to put in my Github
by
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Depending on contractual obligations (writing as an industry employee) sharing code can be a breach of confidentially agreements. Personall…
Answer: Is it possible to annotate a file for the human genome using the command line wi
by
GenoMax
99k
As shown in the [**README**][1], `provean` should run on the command line. [Download][2] and follow install directions. This program requir…
Comment: correlation analysis of a single variable versus multiple variables
by
ATpoint
47k
> My results will be strong enough for a publication? If you plan to publish a few correlation tables for a single gene then the answer is…
Comment: Converting Braker2 gtf output to gff then genbank
by
robert.murphy
▴ 40
Oh it is simply whether the DNA is circular or linear, I thought it was something more complicated like chromatin organisation! Thank you.
Comment: Does GISAID fasta files contain spike protein or whole genome sequence?
by
Devon Ryan
98k
Why not look at the file and find out? You have the sequences, figure it out.
Comment: Converting Braker2 gtf output to gff then genbank
by
Juke34
★ 5.3k
You can get some information calling the EMBLmyGFF3 adanced help: ``` EMBLmyGFF3 --advanced_help topology ``` Otherwise you can find verbo…
Comment: Converting Braker2 gtf output to gff then genbank
by
robert.murphy
▴ 40
In `EMBLmyGFF3` script should I concern myself much with the `topology` option? If yes do you have suggestions for good places to educate (…
Comment: Why GC content is important on NIPT results?
by
German.M.Demidov
★ 2.0k
NIIPT can be performed in various variations and for different purposes. Is it chromosome abnormalities test in your case? If so, extreme G…
Comment: bedops wig2bed 'Row begins with a tab or space' error
by
a_bis
• 0
The output looks as follows: 1^I0^I3000060^I0.000000$ 1^I3000060^I3000090^I0.224911$ 1^I3000090^I3000120^I0.449820$ 1^I30…
Comment: Samtools view filter by reference sequence
by
maxrwjones898
• 0
Thanks for your answer, I will give this a go!
Answer: Variant calling from comparison of assembled genomes where there is only one r
by
Hans
▴ 120
It appears that bcftools takes into consideration the alignments of all genotypes when it calls variants. When I call the variants separat…
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