cd /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_decaurelia-223/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie-build -f pdecaurelia_mac_223_v1.0.fa pdecaurelia_mac_223_v1.0
cd /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_dodecaurelia-274/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie-build -f pdodecaurelia_mac_274_v1.0.fa pdodecaurelia_mac_274_v1.0
cd /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_jenningsi-M/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie-build -f pjenningsi_mac_M_v1.0.fa pjenningsi_mac_M_v1.0
cd /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_novaurelia-TE/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie-build -f pnovaurelia_mac_TE_v1.0.fa pnovaurelia_mac_TE_v1.0
cd /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_polycaryum_Hb20-6/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie-build -f ppolycaryum_mac_Hb20-6_v1.0.fa ppolycaryum_mac_Hb20-6_v1.0
cd /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_quadecaurelia-N1A/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie-build -f pquadecaurelia_mac_NiA_v1.0.fa pquadecaurelia_mac_NiA_v1.0
cd /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_septaurelia-38/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie-build -f pseptaurelia_mac_38_v1.0.fa pseptaurelia_mac_38_v1.0
cd /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_tredecaurelia-AP38/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie-build -f ptredecaurelia_209_AP38_filtered.fa ptredecaurelia_209_AP38_filtered