what is the input for cuffmerge???

Question

[zizigolu]

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

Answer 1

[GouthamAtla]

The output of cufflinks is transcripts.gtf . 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,

[zizigolu]

then how I can create the assemblies.txt file from transcripts.gtf files?

[GouthamAtla]

Open a text editor. copy paste the path to transcripts.gft of each sample per line. Then save the file as assemblies.txt. Or you could also write a short command that does it for you.

[zizigolu]

thank you Goutham

[hamid_fiuji]

thank you for your response, would you please write a command line for cuffmerge and explain each item separately thanks

[zizigolu]

Sorry, I don't have access to Linux or mac I then can't remember what I had done 2 years ago but the instruction of cuffmerge was somehow straightforward as I remember.

[simiyu86wekesa]

Thank you. Your answer is salvation to many