What is the difference between genome fasta file from ENSEMBL and UCSC

Question

[SMILE]

Dears,

I want to know whether there is difference between different genome fasta files like Mus_musculus.GRCm38.dna.toplevel.fa file downloaded from ENSEMBL and chrom_mm10.fa file downloaded UCSC. Whether we can annotate the alignment bam files (using UCSC genome as reference) with ENSEML annotations.

Any comments and explanations are appreciated.

Answer 1

[Emily]

I would suggest reading the README file for the data. Here is the Ensembl one.

Generally, it is recommended that you use reference annotation and genome files from the same source.

[SMILE]

We just realized that our cooperators used the UCSC reference genome mm10, but the further downstream analyses were all using ENSEMBL annotation like TSS, gene start position, gene end position with biomaRt package. Do you think we can keeping on doing this, if not all our previous analyses will start over again.

[Emily]

It's the same genome, so it should be the same. The best place to get the annotation is the GTF or GFF files though, not BioMart, as these should work out of the box with most analysis tools.

[SMILE]

Thank you for the helpful response!

[ATpoint]