I got confused while trying to perform Cuffdiff for my RNA sequencing analysis. 
So I have five different samples which were sequenced. I used tophat to create 
the bam files and cufflink to create the assembled trancripts. Then I uded 
Cuffmerge to merge them in one file and then I wanted to do Cuffdiff with that 
merged file. What shall I choose for the ''SAM or BAM file of aligned RNA-Seq'' 
option? I have the 5 options from the 5 tophat actions on my 5 samples. All I 
want in the end is an excel table showing the number of hits from each sample 
(and not necessary a comparison of them).


Kristis Vevis, PhD Student
Cell Biology
UCL Institute of Ophthalmology
11-43 Bath Street
020 7608 4067

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