Hi there,
I run cuffdiff with two paired-end reads samples and 2 single-end reads samples at the same time the other day(after running tophat toward each samples), and got results which seemed normal and correct with no error messages.
As I read cufflinks, cuffcompare, cuffdiff manuals and didn't find any statements that say they can't treat single-end and paired-end samples together, so I think my results are reliable(I don't know how accurate they are, though).
But I just want to know other RNA-seq users' opinions over cuffdiff's treatment with single/paired-end reads together.
Have anyone done the same analysis before?
I would be very happy if anyone would reply to me and give some advises!
zun
I run cuffdiff with two paired-end reads samples and 2 single-end reads samples at the same time the other day(after running tophat toward each samples), and got results which seemed normal and correct with no error messages.
As I read cufflinks, cuffcompare, cuffdiff manuals and didn't find any statements that say they can't treat single-end and paired-end samples together, so I think my results are reliable(I don't know how accurate they are, though).
But I just want to know other RNA-seq users' opinions over cuffdiff's treatment with single/paired-end reads together.
Have anyone done the same analysis before?
I would be very happy if anyone would reply to me and give some advises!
zun
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