hi friends,

i RNA-seq protocol i read...

tophat -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq

by which i have accepted_hits.bam

cufflinks -p 8 -o C1_R1_clout C1_R1_thout/accepted_hits.bam

then saying that :

Create a file called assemblies.txt that lists the assembly file for each sample. The file should contain the following lines:
./C1_R1_clout/transcripts.gtf
./C2_R2_clout/transcripts.gtf
./C1_R2_clout/transcripts.gtf
./C2_R1_clout/transcripts.gtf
./C1_R3_clout/transcripts.gtf
./C2_R3_clout/transcripts.gtf

then this command

cuffmerge -g genes.gtf -s genome.fa -p 8 assemblies.txt

what is the assemblies.txt please??? how i can create such a file by cufflinks output that as i saw is a file named QC_filtered.fastq

thanks for your simpathy