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Old 07-03-2012, 11:21 AM   #1
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Join Date: Mar 2011
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Default tophat/cufflinks with different read lengths libraries

Dear all,

I have a question about tophat/cufflinks usage and I ask you some suggestions, please!

I have 2 Illumina single end libraries (let's say R1.fastq, R2.fastq) of 2 biological replicates coming from 2 different sequencing runs.

R1.fastq has 72bp reads while R2.fastq has 101bp reads.

We are in doubt whether we should trim the second one to 72bp in order to compare them on the same level or not. I read different opinions about that but I am not convinced yet; after all, read length seems not to be involve in fpkm definition. I also wonder if trimming could even be harmful (reduce correlation between R1 and R2).

Thanks in advance.
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