Hi everyone,
I recently downloaded the histone modifications BAM and broadPeak files for GM12878 cells from UCSC (ENCODE histone modifications > Broad histone) from the link provided below:
http://genome-euro.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHistone
However, the 'Additional Details' column for some of the files states the origAssembly=hg18 while it is hg19 for the others but the 'Alignment' sub-section in the 'Methods' section at the bottom of the page says GRCh37/hg19.
So my question is which human genome assembly (hg18 or hg19) was used for generating these files?
http://genome-euro.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHistone
It seems that every ENCODE data published after January 2011 on UCSC tracks is using hg19.
hg19 is most common now, but all depends on what u r looking for and which question u r answering, using data.
Thanks Kévin and Abhishek for your replies.
I also emailed this question directly to the UCSC team and they confirmed that though the original assembly was different all files have since then been 'lifted over' to the hg19 coordinates.
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