28 results in 0.0031 seconds.
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Remove duplicate genes/mRNA from a gff file
I would like to combine two different gff files and then remove some duplicate genes/mRNA/exons with overlaps. I did not find any tool to do it. There... -
GFF3 formatting wrong for RSEM?
Hello SEQanswers community,
When I run rsem-prepare-reference with refseq it only captures "tRNA" in my gff3 file. I only realized... -
Calculating Read/Coverage Depth per Base Pair from a GFF3 File
Hey, this is my first post and have been searching for hours trying to find a clear answer to this but could not for the life of me. Any input would be...Last edited by dgosting; 10-12-2015, 10:14 PM. -
Problem generating gff3 exon centric annotation to run MISO
I would like to use MISO to extract differential alternative splicing in my rat RNA-SEQ samples, but unfortunately there are not gff3 files for Rat. Has... -
How to know if a SNP is non synonymous using the genome sequence and the gff3 file?
Hi everyone,
Everything is in the title: How to know if a SNP is non synonymous using the genome sequence and the gff3 file?
I have no other... -
Extract gene sequences from gff3 file and reference fasta
Hi,
I have a gff3 file and I want to extract the gene sequences (not including introns). Several genes have many isoforms, but I want only... -
setting GBrowse database and query GFF3
(1) I have uploaded the genome fasta and GFF annotation in the mysql data using following command of Bio:
B::SeqFeature::Store database
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genewise2-4-1（or wise2-4-1） and EVM
I used genewise to alignt a protein set to a genome which I assembled, and I got a GFF3 file. I want to use this GFF3 file to run my EVM, but the GFF3... -
Is this a valid GFF3 file for HTSeq?
Hi there,
I created a gff3 file from GenBank file containing multiple contigs (using Bioperl 'genbank2gff3.pl' tool) . In order to run HTSeq... -
Can anyone recommend software for annotating novel transcripts/genes from Tuxedo
Hi,
I am running RNASeq experiments and identifying and quantifying novel genes and transcripts using a Tudedo pipeline (Bowtie--> TopHat-->... -
Convert gff3 to GRanges
I downloaded the Rnor gff3 from http://mirrors.vbi.vt.edu/mirrors/ft...orvegicus/GFF/ . I can import into R and get it as... -
GFF to introns,
Hello everyone,
I am trying to get intron sequences using gff3 file (from www.phytozome.net) which have coordinates for mRNA, exon, CDS and UTR's.... -
Merge two gff3 files?
I have two gff3 files, one of primary transcripts and one of alternative transcripts, that need to be merged into one file. Since the files must be interwoven... -
Mentor for genome annotation
Anyone here willing to be my mentor, whom i can always refer to when i encounter any problem with my analysis...perhaps someone familiar with genome annotation,... -
Cannot find any mention of reference gff/gtf annotations in cuffmerge output
Hi,
I have been using tophat and cufflinks to analyse some RNA seq data, but cuffmerge is not behaving as I would expect.
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