Transcript Assembly Merge

######15.) CUFFMERGE ######Use Cuffmerge to merge predicted transcripts from all libraries into a unified transcriptome ######Refer to the Cufflinks manual for a more detailed explanation: ######http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge

Cuffmerge basic usage

cuffmerge [options]* <assembly_GTF_list.txt>

<assembly_GTF_list.txt> is a text file "manifest" with a list (one per line) of GTF files that you'd like to merge together into a single GTF file.

######Extra options specified below

'-p 8' tells cuffmerge to use eight CPUs

'-o' tells cuffmerge to write output to a particular directory

'-g' tells cuffmerge where to find reference gene annotations. It will use these annotations to gracefully merge novel isoforms (for de novo runs) and known isoforms and maximize overall assembly quality.

'-s' tells cuffmerge where to find the reference genome files

######Merge all 4 cufflinks results so that they will have the same set of transcripts for comparison purposes

For reference guided mode:

cd $RNA_HOME/expression/tophat_cufflinks/ref_guided/
ls -1 *cDNA*lib*/transcripts.gtf > assembly_GTF_list.txt
cat assembly_GTF_list.txt
cuffmerge -p 8 -o merged -g $RNA_HOME/refs/hg19/genes/genes_chr22.gtf -s $RNA_HOME/refs/hg19/bwt/22/ assembly_GTF_list.txt

For de novo mode:

cd $RNA_HOME/expression/tophat_cufflinks/de_novo/
ls -1 *cDNA*lib*/transcripts.gtf > assembly_GTF_list.txt
cat assembly_GTF_list.txt
cuffmerge -p 8 -o merged -g $RNA_HOME/refs/hg19/genes/genes_chr22.gtf -s $RNA_HOME/refs/hg19/bwt/22/ assembly_GTF_list.txt