Hi,

 

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).

 

Regards  

 

Kristis Vevis, PhD Student

Cell Biology

UCL Institute of Ophthalmology

11-43 Bath Street

London

EC1V 9EL, UK

020 7608 4067

 

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