SEQanswers - View Single Post - problem with tophat commnd directing bowtie indexes

john_mu · 06-16-2010, 09:05 AM

"/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18"

That is wrong

You should point the the bowtie-base, rather than the directory.

eg. something like

"/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18/genome"

06-16-2010, 09:05 AM	#3
john_mu Member Location: Stanford, CA Join Date: May 2010 Posts: 88	"/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18" That is wrong You should point the the bowtie-base, rather than the directory. eg. something like "/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18/genome" __________________ SpliceMap: De novo detection of splice junctions from RNA-seq Download SpliceMap Comment here