Content Comparison

#If you have a local copy:
 cat run_commands/commands.cuffdiff
 
cuffdiff -o diff_out -b reference/genome.fa -p 8 -L C1,C2 -u merged_asm/merged.gtf C1_R1_thout/accepted_hits.bam,C1_R2_thout/accepted_hits.bam,C1_R3_thout/accepted_hits.bam C2_R1_thout/accepted_hits.bam,C2_R2_thout/accepted_hits.bam,C2_R3_thout/accepted_hits.bam
 
#If you don't have a local copy:
cat /corral-repl/utexas/BioITeam/rnaseq_course/cufflinks_results/commands.cuffdiff

#If you have a local copy:
ls -l diff_out
 
#If you don't have a local copy:
cat /corral-repl/utexas/BioITeam/rnaseq_course/cufflinks_results/diff_out

-rwrwxr-rx--r-- 1 daras G-803889      115 May 18 09:48 cds.diff
-rw-r--r--801020  2691192 Aug 21 12:20 isoform_exp.diff  : Differential expression testing for transcripts
-rwxr-x--- 1 daras G-803889801020  1483520 Aug 21 12:20 gene_exp.diff  124 May 18 09:48 cds_exp.diff
-rw-r--r--: Differential expression testing for genes
-rwxr-x--- 1 daras G-803889801020  1729831 Aug 21 12:20 tss_group_exp.diff: Differential 91expression Maytesting 18for 09:48 cds.fpkm_trackingprimary transcripts
-rwrwxr-r-x-r-- 1 daras G-803889801020  273090561369451 MayAug 1821 1312:4220 cuffData.db
-rw-r--rcds_exp.diff      : Differential expression testing for coding sequences
 
-rwxr-x--- 1 daras G-803889801020  14989073277177 MayAug 1821 0912:4820 gene_exp.diffisoforms.fpkm_tracking
-rwrwxr-r-x-r-- 1 daras G-803889801020  16199311628659 MayAug 1821 0912:4820 genes.fpkm_tracking
-rwrwxr-rx--r-- 1 daras G-803889801020  26235811885773 MayAug 1821 0912:4820 isoformtss_expgroups.difffpkm_tracking
-rwrwxr-rx--r-- 1 daras G-803889801020  32380441477492 MayAug 1821 0912:4820 isoformscds.fpkm_tracking
 
-rwrwxr-r-x-r-- 1 daras G-803889801020  11683221349574 MayAug 1821 0912:4820 promoterssplicing.diff  : Differential splicing tests
-rwrwxr-rx--r-- 1 daras G-803889801020  13464111158560 MayAug 1821 0912:4820 splicingpromoters.diff : Differential promoter usage
-rwrwxr-rx--r-- 1 daras G-803889801020   1730507919690 MayAug 1821 0912:48 tss_group_exp20 cds.diff -rw-r--r-- 1 daras G-803889  1887841 May: 18Differential 09:48 tss_groups.fpkm_trackingcoding output