All these steps have already been run. We'll be spending time looking at the commands and output. Let's get set up.
Get to the data
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and results
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cd /corral-repl/utexas/BioITeam/rnaseq_course/cufflinks_exercise |
Step 1: Run tophat2
We've already gone over how this is done and looked over the results. Let's move on to step 2.
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| title | General syntax for cufflinks command |
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cufflinks [options] <hits.bam>
Some of the important options:
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-p/--num-threads
-G/--GTF
-g/--GTF-guide
-b/--frag-bias-correct
-u/--multi-read-correct |
Look a t$BI/rnaseq_course/cufflinks_exercise/run_commands/commands.cufflinks.commands to see how it was run.
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| How do I look into the file? |
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| How do I look into the file? |
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cat $BI/ ngsrnaseq_course/ tophatcufflinks_ cufflinksexercise/run_commands/commands.cufflinks .commands |
Take a minute to look at the output files produced by one cufflinks run.
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| title | Cufflinks output files |
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cd $BI/ngsrnaseq_course/tophatcufflinks_cufflinksexercise/result/C1_R1_clout
ls -l
drwxrwxr-x 2 nsabell G-801021 32768 May 22 15:10 cuffcmp
-rwxr-xr-x 1 daras G-803889 14M Aug 16 12:49 transcripts.gtf
-rwxr-xr-x 1 daras G-803889 597K Aug 16 12:49 genes.fpkm_tracking
-rwxr-xr-x 1 daras G-803889 960K Aug 16 12:49 isoforms.fpkm_tracking
-rwxr-xr-x 1 daras G-803889 0 Aug 16 12:33 skipped.gtf
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cd $BI/ngs_course/tophat_cufflinks
find . -name transcripts.gtf > assembly_list.txt
cuffmerge <assembly_list.txt>
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| assembly_list.txt contents |
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| assembly_list.txt contents |
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cat $BI/ngsrnaseq_course/tophatcufflinks_cufflinksexercise/assembly_list.txt
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Take a minute to look at the output files produced by cuffmerge. The most important file is merged.gif, which contains the consensus transcriptome annotations cuffmerge has calculated.
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cd $BI/ngsrnaseq_course/tophatcufflinks_cufflinksexercise/merged_asm
ls -l
-rwxrwxr-x 1 daras G-803889 1571816 Aug 16 2012 genes.fpkm_tracking
-rwxrwxr-x 1 daras G-803889 2281319 Aug 16 2012 isoforms.fpkm_tracking
drwxrwxr-x 2 daras G-803889 32768 Aug 16 2012 logs
-r-xrwxr-x 1 daras G-803889 32090408 Aug 16 2012 merged.gtf
-rwxrwxr-x 1 daras G-803889 0 Aug 16 2012 skipped.gtf
drwxrwxr-x 2 daras G-803889 32768 Aug 16 2012 tmp
-rwxrwxr-x 1 daras G-803889 34844830 Aug 16 2012 transcripts.gtf
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