RUM and Bowtie2

[katharinedickson]

Hi!

I am running Bowtie2, not Bowtie, on my setup; is it possible to modify any of the programs once RUM is installed to enable RUM to run with Bowtie2? I am getting these error messages:

Can't exec "bowtie-build": No such file or directory at /home/kdickson/Alignment/rum-2.0.5_06/bin/create_indexes_from_ensembl.pl line 135.
Couldn't run 'bowtie-build botznik-chr/botznik-chr_one-line-seqs.fa botznik-chr/botznik-chr_genome': No such file or directory at /home/kdickson/Alignment/rum-2.0.5_06/bin/create_indexes_from_ensembl.pl line 135.

[greggrant]

Hi Katherine thanks for your interest in RUM however unless you have a compelling reason I would recommend using STAR or GSNAP at this point, RUM has not quite kept up with those efforts, mainly due to a lack of manpower. But if you are dead set on using RUM you'll have to install bowtie1, we tried to use bowtie2 under the hood but it really did not perform well, it massively increased the multi-mappers which just did not make sense. Thanks, Greg

[elbakrifz]

I'm running util/mappability/generateMap.pl -w 35 -i /Users/mac/Desktop/NGS-/TriTrypDB-47_LmajorLV39c5_Genome.fasta > /Users/mac/Desktop/NGS-/TriTrypDB-47_LmajorLV39c5_Genome-map.bigwig and I get Can't exec "bowtie": Not a directory at util/mappability/generateMap.pl line 105.
how should I fix it