param	value
cmd_line	cuffdiff -p 20 -o /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/CuffDiff/All/ -b /db/igenomes/Mus_musculus/Ensembl/NCBIM37/Sequence/WholeGenomeFasta/genome.fa -p 8 -L C57,BTBR,Shank3wt,Shank3ko,Caspr2wt,Caspr2ko,Chr16wt,Chr16df --library-type fr-unstranded -u /db/igenomes/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/C57_25_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/C57_26_all.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/C57_27_all.bam /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/BTBR_28_all.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/BTBR_29_all.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/BTBR_30_all.bam /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/shank3wt_37_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/shank3wt_38_all.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/shank3wt_39_sub.bam /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/shank3ko_40_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/shank3ko_41_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/shank3ko_42_all.bam /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/caspr2wt_32_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/caspr2wt_33_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/caspr2wt_31_sub.bam /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/caspr2ko_34_all.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/caspr2ko_35_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/caspr2ko_36_all.bam /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/chr16wt_43_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/chr16wt_44_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/chr16wt_45_sub.bam /users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/chr16df_46_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/chr16df_47_sub.bam,/users/bi/projects/Milana_Morgenstern/Evan_Elliott/2014-10_autism/TopHat/SubSampled/chr16df_48_sub.bam 
version	2.2.1
SVN_revision	4237
boost_version	104700