Consistency Between Bowtie, Tophat And Cufflinks Versions

Question

[narges]

Hi all, I have a general question and I wanted to know your opinion. I know when choosing tophat version, there is restriction to choose the same Bowtie version so Bowtie 1 works with Tophat 1 and the same is for version 2. But how about choosing cufflinks version is there the same restriction or do you have any ideas that in which options the results of combining different versions would be more meaningful or not. Thank you in advance

Answer 1

[JC]

Well, Tophat 2 can work with Bowtie 1 too, Cufflinks is more independent, it can work with any BAM file. I think the question you need to answer is how good is your read mapping, how many reads are aligned, how many reads are located in more than one position, how many genes are covered. I suggest to run some tests to see which combinations it's better.