Hi all,
I've posted this to the Cufflinks mailing list as well:
I'm running cuffdiff v2.2.1 from the binary on both Linux and osx. When I try to use the --multi-read-correct flag, the only difference I see in any output file is the "run.info" where it lists that I used the flag. I can see a second progress bar in the log when it runs with --multi-read-correct, so it looks like cuffdiff recognizes the flag. Otherwise, I can diff any other output with/without multi-read correction and it shows no change. I've tried all the binaries since 2.0.0 and this behavior seems to have started in 2.1.0.
I've also noticed that multi-reads that map to duplicated genes in the genome lead to an FPKM and count of 0 for each duplicate. I'll post after this with concrete examples.
Does anyone else notice no change in their output when enabling or disabling "--multi-read-correct" with cuffdiff 2.2.1?
Michael Leonard
I've posted this to the Cufflinks mailing list as well:
I'm running cuffdiff v2.2.1 from the binary on both Linux and osx. When I try to use the --multi-read-correct flag, the only difference I see in any output file is the "run.info" where it lists that I used the flag. I can see a second progress bar in the log when it runs with --multi-read-correct, so it looks like cuffdiff recognizes the flag. Otherwise, I can diff any other output with/without multi-read correction and it shows no change. I've tried all the binaries since 2.0.0 and this behavior seems to have started in 2.1.0.
I've also noticed that multi-reads that map to duplicated genes in the genome lead to an FPKM and count of 0 for each duplicate. I'll post after this with concrete examples.
Does anyone else notice no change in their output when enabling or disabling "--multi-read-correct" with cuffdiff 2.2.1?
Michael Leonard
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