Hello everyone,
I write to you because we have done a RNAseq analysis from samples of chickens. Our problem is that we have used a genome of reference for the mapping process older (Galgal 4:http://jul2016.archive.ensembl.org/Gallus_gallus/Info/Index ) than the new version (GRCg6a: http://www.ensembl.org/Gallus_gallus/Info/Index ). There is any way to know the equivalence between the old and the new version of the reference assembly?
Thank you very much
Hi Albert
main changes will be annotations and positions.
you can use one of the UCSC web tools to go from a genome to an other one (http://genome-euro.ucsc.edu/cgi-bin/hgLiftOver?hgsid=234175588_YCqKfdMadfMNWI0RzMOkWVmknSbs) by the leftover tool. just choose the start genome and assembly and the destination one.
fred
Hi Albert
main changes will be annotations and positions.
you can use one of the UCSC web tools to go from a genome to an other one (http://genome-euro.ucsc.edu/cgi-bin/hgLiftOver?hgsid=234175588_YCqKfdMadfMNWI0RzMOkWVmknSbs) by the leftover tool. just choose the start genome and assembly and the destination one.
fred
Hi Albert Perlas Puente ,
I agree with the suggestion of Frederic Lepretre .
You can use https://genome.ucsc.edu/cgi-bin/hgLiftOver , which is a tool from UCSC. From that, you can select the original assembly of your sequencing data (which is galGal4 in your case) and select the new assembly, to which your original assembly is to be converted. You can upload your input sequence file in BED format.
Regards,
Greeshma Thulasi
Thank you very much for the help!! Frederic Lepretre Greeshma Thulasi
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