Transcript Assembly Merge

#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 would 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 cDNAlib*/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 cDNAlib*/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