Question: Hg19 Reference Gnome For Tophat2
0
Sachit Adhikari • 320 wrote:
I downloaded the entire directory of UCSC for the reference gnome of
Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same
reference
gnome. I found a directory:
Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
with the files:
genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2
genome.rev.1.bt2
genome.rev.2.bt2
While adding the reference gnome, I need to edit bowtie2_indices.loc
Shall I replace:
/orig/path/hg19 hg19 hg19
/depot/data2/galaxy/bowtie2/hg19/hg19
with
hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
Thanks,
Sachit