Hi All,
I was wondering if anyone could help me running GSNAP, I assume I've got a fairly simple problem.
I first used gmap_build to build a reference
gmap_build -d /Users/kjames/Documents/Chapter5NGS/ROD/GMAP/ RODRef.fasta
And then when I try to run GSNAP it has problems finding -d
gsnap -d /Users/kjames/Documents/Chapter5NGS/ROD/GMAP/ -m 5 -A sam RODc_1.fastq RODc_2.fastq
And it gives the error:
Unable to find genome directory /usr/local/share//Users/kjames/Documents/Chapter5NGS/ROD/GMAP. Either recompile the GMAP package
to have the correct default directory (seen by doing gmap --version),
or use the -D flag to gmap to specify the correct genome directory.
I'm wondering if it's hidden the reference elsewhere but I can't see an obvious location.
Any help would be great appreciated,
Kat
I was wondering if anyone could help me running GSNAP, I assume I've got a fairly simple problem.
I first used gmap_build to build a reference
gmap_build -d /Users/kjames/Documents/Chapter5NGS/ROD/GMAP/ RODRef.fasta
And then when I try to run GSNAP it has problems finding -d
gsnap -d /Users/kjames/Documents/Chapter5NGS/ROD/GMAP/ -m 5 -A sam RODc_1.fastq RODc_2.fastq
And it gives the error:
Unable to find genome directory /usr/local/share//Users/kjames/Documents/Chapter5NGS/ROD/GMAP. Either recompile the GMAP package
to have the correct default directory (seen by doing gmap --version),
or use the -D flag to gmap to specify the correct genome directory.
I'm wondering if it's hidden the reference elsewhere but I can't see an obvious location.
Any help would be great appreciated,
Kat
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