Hi, everyone.
I am in trouble converting gff format file to genbank format.
The gff format file looks like:
Scaffold_15;HRSCAF=18|...
40 results in 0.0032 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... -
Gene cluster identification using gff file
Hello everyone.
I have a list of genes. I want to know which of these are separated by nomore than eight genes (not present in the gene list)... -
gene overlaps in Arabidopsis GFF file
Has anyone ever looked at a GFF to find all the genes that have base overlaps ?
These genes can be counted a 0 in HTSeq and Arabidopsis is a dense... -
htseq-count ERROR in GFF File?
Hello guys,
I'm trying to do a summary of counts in usegalaxy.org. I convert Fatq groomer to sam with Map with BWA for Illumina (Galaxy... -
Tophat transcriptome indexing
Hi,
I'm trying to use tophat on some data and am having an issue. I want to make a transcriptome mapping file like this:
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Something wrong in FlyBase's gtf (gff to gtf conversion)
Hi All,
I wanted to re-create FlyBase's gtf (FB2015_04) from the gff file. It is a different matter why I want to do that.
... -
converting infernal -tblout output to gff
Dear all,
I have run cmsearch from infernal 1.1 to annotate non-coding RNAs in my genome of interest.
With the option --tblout I... -
Get annotations by matching a fasta file to gff
I have a collapsed fasta files with all my counts and the corresponding sequences. I would like to annotate those sequences onto a gff file to find out... -
GMAP problems: stopping at "Finished checking compiler assumptions"
Edit:
Never mind. It was a simple database error. Fixed it, but don't know how to delete post...
I am trying to map around 300 cDNA...Last edited by JonB; 04-28-2015, 08:03 AM. -
Negative interval length in GFF file
I have been given some GFF files to process, and one of these is throwing an error when I attempt to run it through HTSeq-count:
Error... -
Using HTSeq-count when no attributes are available?
I have been using htseq-count with great success, except for one particular type of genome feature, the transposable elements (te).
There is no... -
creating GFF file from refernce fasta
HI,
I am working a flatworm for which the reference genome is not well characterized. I found the refernece trancriptome for my species... -
convert gff to embl/genbank
Dear forum members,
I want to convert gff file to a genbank or a embl format.
Please suggest appropriate for it.
I have Bioperl...Last edited by bio_informatics; 02-06-2014, 11:03 PM. -
Tandem repeats in gff/gtf format
Hi,
I am trying to find tandem repeats (mainly SINE,LINE, ERV) position in gff/gtf format. I don't know if such files exist but i will...
