Hello

I have somehow naive questions.

I have two conditions which I would like to compare. In each condition, we have three replicates.

When, I try to do the cuffmerge command (based on nature protocol paper, 2012,

assemblies.txt file says

./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

but I think that the second and fourth lines should be changed as follows.. Is it right? (I am not sure)

(since current Corrigendum doesn't mention about it, I am wondering whether I am right or not..)

./C1_R1_clout/transcripts.gtf
./C2_R1_clout/transcripts.gtf
./C1_R2_clout/transcripts.gtf
./C2_R2_clout/transcripts.gtf
./C1_R3_clout/transcripts.gtf
./C2_R3_clout/transcripts.gtf

Also, cuffdiff command,

cuffdiff \
  -o diff_out \
  -b genome.fa \
  -p 8 \
  -L C1,C2 \
  -u merged_asm/merged.gtf \
  ./C1_R1_thout/accepted_hits.bam,./C1_R2_thout/accepted_hits.bam,./C1_R3_thout/ accepted_hits.bam \
  ./C2_R1_thout/accepted_hits.bam,./C2_R3_thout/accepted_hits.bam,./C2_R2_thout/ accepted_hits.bam

changed to:

cuffdiff \
  -o diff_out \
  -b genome.fa \
  -p 8 \
  -L C1,C2 \
  -u merged_asm/merged.gtf \
  ./C1_R1_thout/accepted_hits.bam,./C1_R2_thout/accepted_hits.bam,./C1_R3_thout/ accepted_hits.bam \
  ./C2_R1_thout/accepted_hits.bam,./C2_R2_thout/accepted_hits.bam,./C2_R3_thout/ accepted_hits.bam

Is it right? OR I am missing something?

I realized that the order of gtf file in assemblies.txt makes difference in cuffmerge result.

So, I want to make sure I am right..

Thanks in advance