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Showing top results for tag: annotation • reset
0
votes
2
replies
75
views
How to modify right annotation in heatmap without changing the rest of parameters
annotation complexHeatmap heatmap
updated 1 day ago by 107k • written 1 day ago by • 0
0
votes
0
replies
38
views
Annotation for copy number called segments from VarScan 2 output.
Annotation Copy VarScan2 Segmentation CNVs Number
2 days ago by TanayB • 0
3
votes
3
replies
494
views
Is there a way to find the GWAS traits to a gene programmatically?
gwas api gene annotation gwascatalog
2 days ago by cmcouto.silva ▴ 40
0
votes
1
reply
64
views
BLAST Annotating Sub-sequences of Features with Not Normalized Identity Scores
BLAST Annotation
updated 3 days ago by ▴ 380 • written 3 days ago by • 0
3
votes
5
replies
367
views
Why some SNP's are not assigned to any gene?
annotation gene SNP
updated 4 days ago by ★ 2.5k • written 7 days ago by • 0
0
votes
0
replies
50
views
Error in Demovir
metagenomics ngs annotation taxonomy virome
8 days ago by ernie7417 • 0
8
votes
11
replies
4.0k
views
7 follow
snpEFF not able to download GRCH38 ?
Annotation genome
updated 9 days ago by ▴ 190 • written 3.6 years ago by ▴ 130
1
vote
1
reply
112
views
Refseq annotation for processed/unprocessed Pseudogenes
refseq pseudogene annotation genomics
updated 9 days ago by 107k • written 10 days ago by ▴ 30
0
votes
2
replies
171
views
Genome mapping and annotation
annotation genome
10 days ago by claudia • 0
0
votes
0
replies
92
views
Job: Post-doctoral position in bioinformatics for the analysis of enzyme families from metagenomic data, Evry, France
enzyme functional annotation bioinformatics postdoc metagenomic
10 days ago by vallenet • 0
0
votes
0
replies
35
views
Job: Post-doctoral position in bioinformatics for the analysis of enzyme families from metagenomic data, Evry, France
enzyme functional annotation bioinformatics postdoc metagenomic
10 days ago by vallenet • 0
0
votes
1
reply
174
views
Why do annotating the same functionality with different databases produce different results？
kegg annotation eggnog metagenomic
updated 11 days ago by 25k • written 11 days ago by ▴ 10
2
votes
6
replies
405
views
6 follow
Extracting exons and transcripts from gff3/gtf
assembly gtf annotation gff3
9 days ago by mglasena ▴ 30
0
votes
0
replies
112
views
Convert between UCSC gene id(?) and gene symbol with bioconductor
annotation bioconductor
13 days ago by kevin.stachelek ▴ 10
0
votes
19
replies
600
views
Plant Genome Annotation
Genome Annotation
14 days ago by hafiz.talhamalik ▴ 320
0
votes
1
reply
104
views
How is better perform the analyze the somatic mutations? (the mutations of my interest gene)
somatic VCF annotation Oncoplot
updated 15 days ago by ★ 2.5k • written 15 days ago by • 0
0
votes
0
replies
63
views
What is the difference between GERP S and GERP N?
annotation GERP pathogenic genomics
17 days ago by DN99 • 0
1
vote
2
replies
163
views
Specifications for annotation names or symbols?
specification annotation
17 days ago by Alex Reynolds 33k
4
votes
4
replies
260
views
Good or bad idea to annotate with newer genome build?
array methylation beadchip build annotation
14 days ago by Pratik Mehta ▴ 580
7
votes
6
replies
623
views
Can non-driver mutations disrupt the function of proteins and further affect a cellular pathway?
driver somatic annotation VCF oncoplot
updated 18 days ago by ▴ 970 • written 19 days ago by ▴ 20
1
vote
4
replies
249
views
Case Control count per variant
WGS VCF Annotation NGS
21 days ago by williamsbrian5064 ▴ 390
1
vote
1
reply
147
views
GWAS results: base pair annotation
GWAS Annotation results
15 days ago by hemasekhar09 • 0
2
votes
4
replies
1.0k
views
List of human protein coding genes with given name (known function?)
RNA-Seq Annotation Human
updated 22 days ago by ★ 8.8k • written 2.1 years ago by ★ 2.5k
0
votes
6
replies
467
views
How to perform gene annotation in kallisto?
Gene kallisto annotation
25 days ago by synat.keam • 0
1
vote
14
replies
741
views
7 follow
Looking tools for genes annotation
Genome annotation
updated 26 days ago by 12k • written 27 days ago by • 0
0
votes
0
replies
72
views
How to determine exact tRNA sequence
annotation
4 weeks ago by wes ▴ 50
0
votes
0
replies
79
views
Annotation Forge Error: makeOrgPackageFromNCBI
annotation forge
4 weeks ago by Trinh • 0
0
votes
0
replies
149
views
liftoff (for lift-over GFF or GTF ) UnboundLocalError: local variable 'feature_db' referenced before assignment
gtf gff3 liftoff annotation comparative_genomics
4 weeks ago by kofuji • 0
0
votes
1
reply
138
views
Sequence search parameters for annotation of de novo transcriptomes
annotation transcriptome search blast
updated 5 weeks ago by 4.9k • written 5 weeks ago by ★ 1.5k
6
votes
2
replies
300
views
Forum: Sequence (annotation) databases in 2021
uniprot annotation sequence ensembl ncbi
updated 5 weeks ago by ★ 1.7k • written 5 weeks ago by ★ 1.5k
1
vote
2
replies
210
views
How to fix GTF files by adding specific strings into empty gene_id ""
cellranger GTF Annotation UNIX
29 days ago by sasa ▴ 10
0
votes
1
reply
124
views
Using protein domains for annotation validation
Interpro annotation domain InterproScan
updated 5 weeks ago by 25k • written 5 weeks ago by ▴ 430
2
votes
5
replies
428
views
MAKER genome annotation error with SNAP ab initio prediction
SNAP annotation genome MAKER
updated 5 weeks ago by 7.3k • written 6 weeks ago by ▴ 110
3
votes
2
replies
246
views
How can I add KEGG functional categories to whole genome alignments?
alignment annotation technical
5 weeks ago by Ssri • 0
1
vote
12
replies
1.1k
views
7 follow
Error when trying to import GTF files using rtracklayer's import function
annotation rtracklayer software error
5 weeks ago by Marcel • 0
1
vote
3
replies
276
views
Analysing RNA seq data
rna-seq annotation bioconductor
updated 6 weeks ago by ▴ 10 • written 6 weeks ago by ▴ 20
2
votes
5
replies
365
views
Manual annotation of cell types in single cell RNA-seq
Seurat single_cell annotation
updated 6 weeks ago by 7.5k • written 6 weeks ago by ▴ 210
1
vote
12
replies
1.7k
views
How to get KEGG pathway names in KEGG enrichment analysis using clusterprofiler
annotation enrichment KEGG clusterprofiler RNA-Seq
updated 6 weeks ago by ★ 2.5k • written 17 months ago by ▴ 120
1
vote
1
reply
192
views
Detecting and masking repeats with EDTA: Low threshold vs complete masking
repeat masker. annotation genome EDTA
updated 6 weeks ago by ▴ 20 • written 10 weeks ago by • 0
1
vote
2
replies
223
views
question about Mutation Annotation Format (MAF) variant classifications
annotation ICGC MAF R
6 weeks ago by Charles Murtaugh ▴ 20
13
votes
15
replies
8.5k
views
6 follow
Where To Find Annotation File For Agilent Microarray?
annotation
updated 6 weeks ago by ▴ 20 • written 8.2 years ago by ★ 1.1k
2
votes
0
replies
106
views
eggNOG v5 annotation file
eggNOG Annotation
7 weeks ago by Mehmet ▴ 710
0
votes
2
replies
223
views
Variant annotation using VEP
Annotation Zygosity VEP
7 weeks ago by nkausthu ▴ 30
0
votes
0
replies
101
views
Annovar output no comment column?
annovar GWAS annotation Annovar Post-GWAS
7 weeks ago by okiedokie1208 ▴ 30
2
votes
4
replies
308
views
interpreting heatmap on metascape
heatmap metascape excel page annotation terms enriched
4 weeks ago by fionajcunningham • 0
3
votes
9
replies
2.4k
views
Using VEP to get gnomAD frequencies
annotation frequency allele frequency vep gnomAD
updated 8 weeks ago by • 0 • written 2.7 years ago by ▴ 30
0
votes
0
replies
75
views
What should I write after --operation in ANNOVAR for my interest database ?
ANNOVAR CIViC annotation DoCM VCF
8 weeks ago by Zahra ▴ 20
1
vote
4
replies
236
views
How to get from annotated sequences to UniProt IDs
annotation
updated 8 weeks ago by ★ 1.0k • written 8 weeks ago by ▴ 50
2
votes
2
replies
232
views
Tool: miRAnno—network-based functional microRNA annotation
pathways miRNA annotation microRNA
8 weeks ago by tomastokar ▴ 50
4
votes
6
replies
481
views
6 follow
What is the best annotation tool?
VCF annotation
updated 8 weeks ago by ★ 3.1k • written 8 weeks ago by • 0
50 results • Page 1 of 1
Recent Votes
Comment: Per sequence GC content still not good after trimming
Answer: Dealing with missing values in population allele frequency data in classifier m
Comment: Linux for Biologists e-book (free to read online)
Comment: Weird error from BWA and BOWTIE2
Answer: Weird error from BWA and BOWTIE2
Comment: Weird error from BWA and BOWTIE2
Answer: Generating volcano plots of high and low expressed gene in scRNAseq data?
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Recent Replies
Answer: edgeR design matrix error not of full rank by swbarnes2 11k
You can't do group and gender together, because all your "_man" samples are all men and all your "_woman" are all women. Pick group or gen…
Comment: How to perform DE anaysis on a data set in which biological replicates have high by swbarnes2 11k
You "can", but is it best practice? "5 biological replicates" shouldn't mean "5 different cell lines". It should mean "5 samples that are…
Comment: Per sequence GC content still not good after trimming by GenoMax 107k
A simple naive explanation can be that you have fragments in your data that contain more GC that most other fragments. That could simply be…
Comment: Per sequence GC content still not good after trimming by zouini6 • 0
I don't know if it's a rich GC organism. I am moving along with the analyses but I just wanna know what are the potential interpretation fo…
Comment: Per sequence GC content still not good after trimming by GenoMax 107k
Is the organism you are working on GC rich? At this point in process I suggest that you move along with the analysis. If concerns crop up i…
Comment: Error: mdb_env_open: Bad file descriptor by vasudha • 0
okay. I am defining all the paths correctly.
Comment: Error: mdb_env_open: Bad file descriptor by vasudha • 0
I checked, all the files have write permissions and there's memory as well. Do line `496 in update_blastdb.pl` refers to anything related …
Comment: Compare two VCF files in Python by Ram 34k
>It doesn't work This is not sufficient description of failure. Show us sample data, expected results, actual results and the difference.
Answer: Dealing with missing values in population allele frequency data in classifier m by Hamid Ghaedi ★ 1.7k
I thought to share what I found as solution for this problem here, so it might be helpful for someone else as well. The python package `X…
Comment: BCFtools view -R function by Ram 34k
I'd recommend splitting multi-allelics and left-aligning the VCF before doing the operation. Your data looks transposed to me - is that so…
Comment: Linux for Biologists e-book (free to read online) by Ram 34k
You could add a way to donate, both as a small compensation for your effort as well as for any upkeep operations. The Biostar Handbook work…
Comment: How to find differences between single cell RNA seq samples beyond cluster infor by ATpoint 54k
I would take the findings that you have and try to build a hypothesis for downstream validation or functional testing. These single-cell ap…
Answer: How to find differences between single cell RNA seq samples beyond cluster infor by andrew.j.skelton73 6.3k
Providing you have replication, one could test for proportional expansion / contraction of a given cell type. If you're confident in the bi…
Comment: Weird error from BWA and BOWTIE2 by SkyL ▴ 10
thanks for the quick response, but what confused me is that for the same data, **bwa mem** finished without error but **minimap2** got such…
Comment: Weird error from BWA and BOWTIE2 by Mensur Dlakic ★ 13k
`SEQ and QUAL are of different length` message points to a different problem, and that could be an issue with a simulator rather than memor…
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