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Showing top results for tag: gtf • reset
6
votes
8
replies
465
views
Are there any alternatives to Liftoff - Mapping annotations (GFF/GTF) between assemblies
annotations mapping GTF GFF3
updated 11 days ago by ★ 6.3k • written 25 days ago by ▴ 60
2
votes
6
replies
420
views
6 follow
Extracting exons and transcripts from gff3/gtf
assembly gtf annotation gff3
12 days ago by mglasena ▴ 30
3
votes
6
replies
344
views
gffread error
gtf gff gffread
20 days ago by rhksgudbc • 0
3
votes
9
replies
459
views
snpeff : wont recognize the gtf or gff3 files (runtime exception)
GTF GFF3 snpeff
23 days ago by VenGeno ▴ 60
0
votes
0
replies
151
views
liftoff (for lift-over GFF or GTF ) UnboundLocalError: local variable 'feature_db' referenced before assignment
gtf gff3 liftoff annotation comparative_genomics
5 weeks ago by kofuji • 0
1
vote
2
replies
211
views
How to fix GTF files by adding specific strings into empty gene_id ""
cellranger GTF Annotation UNIX
4 weeks ago by sasa ▴ 10
0
votes
4
replies
304
views
cellranger count aggregated to transcripts
cellranger gtf 10x
updated 8 weeks ago by ★ 2.5k • written 8 weeks ago by ▴ 620
1
vote
4
replies
376
views
RNAseq - GBFF cannot be converted to GTF
Genome GBFF GTF NCBI RNAseq
9 weeks ago by sacdefruits • 0
0
votes
0
replies
103
views
GFF/GTF: how to translate CDS genomic coordinates to protein coordinates
GTF GFF3
updated 9 weeks ago by ★ 6.3k • written 9 weeks ago by ★ 1.2k
0
votes
2
replies
244
views
How to retrieve a specific version of Araport annotation file?
Arabidopsis gtf annotations
10 weeks ago by Hojn • 0
3
votes
4
replies
284
views
Using RefSeq gene annotation file to determine gene lengths
refseq rstudio htseq featurelength gtf fpkm geneid
updated 12 weeks ago by ★ 6.3k • written 12 weeks ago by ▴ 10
0
votes
0
replies
142
views
Correct way to write the names in the "product" field of a GTF file
gtf rnaseq annotation
3 months ago by arturo.marin ▴ 10
5
votes
6
replies
381
views
How to generate GTF file from BLAST output?
GTF
3 months ago by mathavanbioinfo ▴ 60
0
votes
1
reply
190
views
Where to get the human mitochondiral reference genome?
GTF human genome mitochondiral
updated 3 months ago by 107k • written 3 months ago by ▴ 60
3
votes
4
replies
379
views
Proportion of RNAseq reads mapping to rRNA, tRNA, mRNA, and intergenic or antisense regions of the genome?
GTF featureCounts NGS GFF
updated 3 months ago by 13k • written 3 months ago by ▴ 60
4
votes
6
replies
353
views
RNA-seq for beginners
reference resequencing transcriptome gtf sequence gff
3 months ago by arko.bmb.du ▴ 20
7
votes
14
replies
1.0k
views
GTF file how do I search for duplicates of Gene ID and print them out
GTF Bash
updated 3 months ago by ▴ 580 • written 3 months ago by ▴ 10
0
votes
1
reply
145
views
How do I correctly add a plasmid sequence with multiple genes to a gtf as well as fasta file?
gtf fasta plasmid
updated 3 months ago by ▴ 150 • written 3 months ago by • 0
0
votes
1
reply
249
views
Extract data from GTF file
gtf java
updated 3 months ago by 34k • written 3 months ago by • 0
1
vote
3
replies
316
views
How to remove repeated sequence region in Interproscan .gff3 with many ORFs?
format region interproscan gff3 gtf
updated 3 months ago by ★ 6.3k • written 3 months ago by • 0
5
votes
6
replies
483
views
Problem with featureCounts using a GTF generated by me
gtf annotation rnaseq
updated 3 months ago by ★ 6.3k • written 3 months ago by ▴ 10
6
votes
4
replies
260
views
Genome annotation file GFF3 and GTF same? interchangeable?
GTF GFF3 NGS ANNOTATION
3 months ago by Akash D ▴ 10
2
votes
2
replies
297
views
Do EGA RNAseq .bam files come with gtf/gff file corresponding to the genome assembly used?
gtf gff RNAseq bam EGA
updated 4 months ago by 107k • written 4 months ago by ▴ 10
0
votes
0
replies
103
views
Create gtf annotations to a fasta file, based on a similar known genome.
sequencing annotations fasta gtf
4 months ago by adi.rotem • 0
2
votes
4
replies
311
views
Merge 2 GTF using agat avoiding overlapping
Merge GTF GFF agat
updated 4 months ago by ★ 6.3k • written 4 months ago by ▴ 190
5
votes
3
replies
313
views
Where I can get the gtf file of antheraea mylitta
GTF
updated 4 months ago by 12k • written 4 months ago by ▴ 60
0
votes
4
replies
287
views
Add all non overlapping genes/transcripts from one gtf to another with bedtools intersect
bedtools annotation gtf
5 months ago by robert.murphy ▴ 50
1
vote
4
replies
450
views
Coordinates long non-coding RNAs
gtf python bedtools rna-seq hg38
5 months ago by luffy ▴ 20
2
votes
1
reply
181
views
How to extract this information
gtf r rna seq galaxy
updated 5 months ago by 8.3k • written 5 months ago by • 0
0
votes
2
replies
203
views
from fasta to gtf format?
gtf DE fasta
updated 5 months ago by 12k • written 5 months ago by ▴ 200
14
votes
1
reply
681
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 5 months ago by 49k • written 5 months ago by ★ 6.3k
3
votes
8
replies
664
views
Convertion Of Gff3 To Gtf
gtf gff
5 months ago by daalsa98 ▴ 10
1
vote
1
reply
265
views
How to merge two GTFs which share some common features
stringtie GTF annotation
updated 5 months ago by 107k • written 5 months ago by • 0
0
votes
0
replies
342
views
my gffcompare out put gtf file is like that. on complete row is followed by some uncomplete row wich have not class codes.
gffcompare rna lncrna gtf
updated 5 months ago by 107k • written 5 months ago by ▴ 10
18
votes
28
replies
1.4k
views
How to combine 2 incomplete GTF
Cufflinks Cuffcompare GTF Cuffmerge Merge
4 months ago by rafaelsolersanblas ▴ 190
5
votes
5
replies
919
views
Which Fasta file and GTF file to use in STAR alignment
STAR ENSEMBL GTF fa
updated 5 months ago by ▴ 140 • written 5 months ago by • 0
2
votes
3
replies
420
views
GTF file and Transcript ID
transcriptid rnaseq gtf
updated 5 months ago by ★ 2.0k • written 5 months ago by ▴ 10
2
votes
2
replies
365
views
Why we have exons that start and end at the same coordinate?!
gtf exon GRCh38
updated 5 months ago by 46k • written 5 months ago by 9.0k
0
votes
0
replies
334
views
Error when making TxDb object from gtf file
gtf Xenopus RStudio TxDb
5 months ago by bowden • 0
3
votes
5
replies
880
views
I could not load GTF data at IGV("Could not create index file") Please help me :)
gtf igvtools igv sort index
updated 5 months ago by 107k • written 5 months ago by • 0
0
votes
7
replies
776
views
Converting genbank to GTF?
gtf genbank
updated 5 months ago by 89k • written 5 months ago by ▴ 10
0
votes
1
reply
319
views
2 transcript_id values for the same tRNA in GTF file
GTF arabidopsisthaliana annotation
updated 6 months ago by 5.4k • written 6 months ago by • 0
11
votes
5
replies
2.3k
views
Tool: AGAT - Another Gff/Gtf Analysis Toolkit
gtf toolkit annotation gff Tool
10 days ago by Juke34 ★ 6.3k
0
votes
2
replies
197
views
Modifying an annotation files after transgene insertion
transgene insertion gtf annotation
6 months ago by Assa Yeroslaviz ★ 1.6k
8
votes
7
replies
336
views
How to add "transcript" feature to a gtf file?
gtf
7 months ago by pomodoro_sinensis ▴ 10
1
vote
2
replies
288
views
editing gtf file
gtf gee edit
updated 8 months ago by 13k • written 8 months ago by ▴ 10
3
votes
4
replies
748
views
Tool: Extend 3' UTR of a GTF file
RNA-Seq annotation GTF python Tool
updated 10 weeks ago by • 0 • written 12 months ago by ▴ 440
0
votes
0
replies
325
views
bedmap to annotate bed file with GTF that was converted to BED produces way too many results
bedmap bed GTF
9 months ago by Tawny ▴ 170
3
votes
3
replies
549
views
Is there any tool/API available to convert GTF/GFF to JSON format?
gtf gff json ncbi ensembl
updated 9 months ago by ★ 2.7k • written 9 months ago by 5.5k
0
votes
3
replies
383
views
How to get transcript ID and tpm from the gtf files of ballgown outputs?
RNA-Seq ballgown hisat2 gtf awk
updated 9 months ago by 34k • written 9 months ago by ▴ 90
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Hi GenoMax, sorry for the late response. Yes I am looking to only keep one hit. I am not sure I follow the idea that all the reported hit…
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Spliced transcripts will bring together ends of exons that may be much farther apart in the genome. A short illumina read can now cover tha…
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