Illumina iGenomes for UCSC, NCBI and Ensembl on Cufflinks webpage

Question

[ndejay]

Hi,

I am trying to count genes using a variety of references. On the following page from the Cufflinks website are listed the following annotation bundles:

• Ensembl/GRCh37
• NCBI/build37.2
• UCSC/hg19

for the human genome. I have two questions concerning what they contain.

1. Is NCBI/build37.2 the same (or equivalent) as NCBI's RefSeq?
2. How modified are each of the bundles with regard to their respective, purported source?

I am speaking mostly of the gtf files provided under Homo_sapiens/${X}/${Y}/Annotation/Genes/genes.gtf.

I am very confused by the number of available annotations. It appears that having too many options can be a curse too ;). I'd very much appreciate it if anyone could shed some light on this matter! Thanks in advance.