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    Rob Patro
    @rob-p
    Hi all --- just to let you know, there's now a dedicated channel for salmon here!
    Nicola Soranzo
    @nsoranzo
    Hi Sailfish devs!
    I need some help in compiling the program while linking to a previously compiled Boost 1.59.0
    Rob Patro
    @rob-p
    What kind of linking error are you seeing?
    Nicola Soranzo
    @nsoranzo
    Rob Patro
    @rob-p
    wow, this is interesting
    it definitely has to do with differences in the compiler
    Nicola Soranzo
    @nsoranzo
    Does Boost need to be compiled with the same version of sailfish?
    Rob Patro
    @rob-p
    Sorry for the delay --- meetings all morning!
    my guess is that the major version change in GCC (5.2.0) has binary incompatibilities with older versions
    do you have access to the compiler that was used for boost?
    Nicola Soranzo
    @nsoranzo
    No problem! Boost was compiled with GCC 4.4.6
    which is not compatible with sailfish
    I can try with 4.9.1 or 5.1.0, if you think that can help
    Nicola Soranzo
    @nsoranzo
    Yes! 4.9.1 seems to work, going to test with 5.1.0 now
    Nicola Soranzo
    @nsoranzo
    5.1.0 gives the same error of 5.2.0
    Rob Patro
    @rob-p
    Great. Yes, I think there was a ABI compatibility change betwen 4.x and 5.x
    Nick Schurch
    @nickschurch
    @rob-p the 'NumReads' field in quant.sf - these are actually estimated counts right, comparable to the kallisto est_counts field?
    Rob Patro
    @rob-p
    Yup; NumReads is the estimate of the number of fragments (a paired-end read counts as 1) originating from each transcript
    Nick Schurch
    @nickschurch
    great, thanks. It seems that the kallisto peeps have fixed their bug and I can now run it on all the data. So, time to compare salmon/sailfish/kallisto across many replicates for three annotations... this is gonna be a data vis challenge!
    Rob Patro
    @rob-p
    Nice! Of course, sailfish is up to 0.9.0 and salmon is up to 0.6.0, so I recommend you compare with the latest versions
    Some improvements, fixes and new features (seq-specific bias correction)
    Will be cool to see the large-scale similarities and dufferences
    Nick Schurch
    @nickschurch
    In the long run, yes. I'm going to use what I have first and - once I've sorted the comparison sensibly - then I'll rerun for new versions ;)