Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Reverted from v. 16

...

Code Block
titleGet set up
cds
cd my_rnaseq_course
cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/cufflinks_results .
 
 
cd cufflinks_results

...

We've already gone over how tophat results look here so let's move on to step 2. 

...

Code Block
titlecommands.cufflinks
#If you've copied it over successfully:
cat run_commands/commands.cufflinks
 
#If you don't have a local copy, you can read it from the source: 
cat /corral-repl/utexas/BioITeam/rnaseq_course_2015/cufflinks_results/run_commands/commands.cufflinks

...

Code Block
titleCufflinks output files
#If you have a local copy:
ls -l C1_R1_clout
 
 
#If you don't have a local copy:
ls -l /corral-repl/utexas/BioITeam/rnaseq_course_2015/cufflinks_results/C1_R1_clout

-rw------- 1 daras G-801020   627673 May 17 16:58 genes.fpkm_tracking
-rw------- 1 daras G-801020  1021025 May 17 16:58 isoforms.fpkm_tracking
-rw------- 1 daras G-801020        0 May 17 16:50 skipped.gtf
-rw------- 1 daras G-801020 14784740 May 17 16:58 transcripts.gtf

...