## myrna commands used to create expressionsets and count tables WITHOUT truncation ## alyssa frazee ## november 1, 2011 $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/bottomly-new/manifest/bottomly.manifest \ --output=s3n://myrna-tmp/bottomly-new/bottomly_output_notrunc \ --reference=s3n://myrna-refs/mouse_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts \ --instances=8 \ --name "bottomly-notrunc" \ --bowtie-args="-v 3 -m 1" \ --gene-footprint=intersect \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/cheung/manifest/cheung.manifest \ --output=s3n://myrna-tmp/cheung/cheung_output_notrunc \ --reference=s3n://myrna-refs/human_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts\ --instances=8 \ --bowtie-args="-v 3 -m 1" \ --gene-footprint=intersect \ --name "cheung-notrunc" \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/hammer/manifest/hammer.manifest \ --output=s3n://myrna-tmp/hammer/hammer_output_notrunc \ --reference=s3n://myrna-refs/rat_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts \ --instances=8 \ --name "hammer-notrunc" \ --bowtie-args="-v 3 -m 1" \ --gene-footprint=intersect \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/katzhuman/manifest/katzhuman.manifest \ --output=s3n://myrna-tmp/katzhuman/katzhuman_output_notrunc \ --reference=s3n://myrna-refs/human_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts \ --instances=8 \ --name "katz-human-notrunc" \ --bowtie-args="-v 2 -m 1" \ --gene-footprint=intersect \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/modencodefly/manifest/modencode-fly.manifest \ --output=s3n://myrna-tmp/modencodefly/modencodefly_output_notrunc \ --reference=s3n://myrna-refs/fly_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts \ --instances=8 \ --name "modencode-fly-notrunc" \ --bowtie-args="-v 3 -m 1" \ --gene-footprint=intersect \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/trapnell/manifest/trapnell.manifest \ --output=s3n://myrna-tmp/trapnell/trapnell_notrunc \ --reference=s3n://myrna-refs/mouse_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts \ --instances=8 \ --name "trapnell-notrunc" \ --truncate=76 --bowtie-args="-v 3 -m 1" \ --gene-footprint=intersect \ --from-middle ##NOTE: the truncate option was used here because this study actually used 76bp paired reads, but the raw .fastq files were not separated into mate1 and mate2 -- instead, mate1 and mate2 were "stuck together" on one line. Truncating was our way of only taking the first mate of the pair. $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/modencodeworm/manifest/modencode-worm.manifest \ --output=s3n://myrna-tmp/modencodeworm/modencodeworm_output_notrunc \ --reference=s3n://myrna-refs/worm_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts \ --instances=8 \ --name "modencode-worm-notrunc" \ --bowtie-args="-v 3 -m 1" \ --gene-footprint=intersect \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/montpick/manifest/montpick.manifest \ --output=s3n://myrna-tmp/montpick/montpick_output_notrunc \ --reference=s3n://myrna-refs/human_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts\ --instances=8 \ --name "Montgomery-Pickrell-notrunc" \ --bowtie-args="-v 2 -m 1" \ --gene-footprint=intersect \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/wang/manifest/wang.manifest \ --output=s3n://myrna-tmp/wang/wang_output_notrunc \ --reference=s3n://myrna-refs/human_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts\ --instances=8 \ --name "wang-notrunc" \ --bowtie-args="-v 2 -m 1" \ --gene-footprint=intersect \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/yang/manifest/yang.manifest \ --output=s3n://myrna-tmp/yang/yang_output_notrunc \ --reference=s3n://myrna-refs/mouse_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts\ --instances=8 \ --name "yang-notrunc" \ --bowtie-args="-v 2 -m 1" \ --gene-footprint=intersect \ --from-middle $MYRNA_HOME/myrna_emr \ --preprocess \ --input=s3n://myrna-tmp/bodymap/manifest/bodymap.manifest \ --output=s3n://myrna-tmp/bodymap/bodymap_output_notrunc \ --reference=s3n://myrna-refs/human_ensembl_61.jar \ --tempdir=/tmp/myrna-afrazee/invoke.scripts \ --instances=8 \ --name "bodymap-notrunc" \ --bowtie-args="-v 3 -m 1" \ --gene-footprint=intersect \ --from-middle