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gff files in kmer analysis.
06-Nov-2017, 04:05 PM
Post: #3
RE: gff files in kmer analysis.
Hi James,

Thanks for quick reply. I looked the bam files of genome mapping and chromosomes start with "chr", ensembl/NCBI gff will not work as there is no "chr" as prefix.

It is difficult to get a gff3 for ucsc annotation.

I will try to upload the ensembl and redo the genome mapping step, and then kmer.


(06-Nov-2017 12:50 PM)jamesp Wrote:  Hello Shao,
we have not tried running kmer on mouse data ourselves. Anyhow the necessary gff file is not available on RiboGalaxy. So you will need to retrieve and upload the gff file yourself. An important recommendation mentioned in another post on this forum is that the genome fasta file and the gff file need to be from the same source and need to refer to the chomosome sequences in the same format . Unfortunately this requirement is not always met for different species from the same library and it is therefore difficult to give a definitive answer. The best advice we can give is to try using files from either Ensembl or NCBI and see what is the outcome.
Thanks to let us know what happens if you try this.

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Messages In This Thread
gff files in kmer analysis. - shao - 06-Nov-2017, 10:04 AM
RE: gff files in kmer analysis. - jamesp - 06-Nov-2017, 12:50 PM
RE: gff files in kmer analysis. - shao - 06-Nov-2017 04:05 PM
RE: gff files in kmer analysis. - shao - 07-Nov-2017, 12:52 PM

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