Tophat2: Ensembl GRCh37 V's UCSC hg19

[SHeaph]

Hi,

I am new to tophat and I would like to know if there is any difference in using the bt2 index files and FASTA file from either Ensembl GRCh37 or UCSC hg19?

Are they the same files?

Thanks in advance.

[westerman]

If there is a difference -- and I do not deal with human genomes very often -- then the difference should be slight. Ensembl says:

Ensembl uses a one-based coordinate system. (UCSC use a zero-based coordinate system.)

Ensembl uses the most recently updated human genome housed at the GRC. This current major assembly release is called GRCh37. NCBI and UCSC use the same genome. (UCSC refers to the recent human genome as GRCh37/hg19

[wyll]

Hi,

Thank you for the explanation.
I was wandering why a variant is one base off in the LMNA gene.

Just one more question,
howcome only a few variants are one base off (ie LMNA gene) while the variants could match in other genes?

Thank you~~