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Code Block
titleCufflinks output files
cd $BI/rnaseq_course/cufflinks_exercise/resultresults/C1_R1_clout
ls -l


drwxrwxr-x 2 nsabell-rw------- 1 daras G-801021801020   627673 32768 May 2217 1516:10 cuffcmp
-rwxr-xr-x58 genes.fpkm_tracking
-rw------- 1 daras G-803889801020  1021025 14MMay Aug17 16 12:4958 transcriptsisoforms.gtf
-rwxr-xr-xfpkm_tracking
-rw------- 1 daras G-803889801020 597K Aug 16 12:49 genes.fpkm_tracking -rwxr-xr-x 1 daras G-8038890 960KMay Aug17 16 12:4950 isoformsskipped.fpkm_trackinggtf
-rwxr-xr-xrw------- 1 daras G-803889801020 14784740 May  0 Aug17 16 12:3358 skippedtranscripts.gtf

Step 3: Merging assemblies using cuffmerge

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