Significant difference between Grch37 and human_g1k_37

Question

[onspotproductions]

Is there much difference as far as gene annotations between these two genome assemblies (Grch37 and human_g1k_37)? I am primarily looking to make sure the ensemble GTF file with the annotations for differential expression will work with either assembly when reads are mapped to it.

Answer 1

[igor]

1000genomes provides an explanation (http://www.1000genomes.org/category/assembly/):

For the phase 1 and phase 3 analysis we mapped to GRCh37. Our fasta file which can be found here called human_g1k_v37.fasta.gz, it contains the autosomes, X, Y and MT but no haplotype sequence or EBV.

Answer 2

[mastal511]

The main thing to check is how the chromosomes are named (e.g. 'chr1' or just '1'), because that always causes problems.

[Jorge Amigo]

this is not correct. the main thing to check is that the reference you're using is exactly what you think you're using. historically, american projects tend to use chr-labeled cromosomes, wether european projects tend to use non-chr-labeled chromosomes. and this hasn't to do with the reference genome of choice.