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
<p>The output of cufflinks is<code> transcripts.gtf</code> . If you have many samples, cufflinks creates transcripts.gtf ( i.e assembles transcripts) file for each samples and these needs to be merged by cuffmerge,</p>
