Question on bootstrap segmentation fault and output

[LiveNKicking]

Hi Everyone,

I am a new to RNA-seq. As such, I am still in  working out a couple of things. Your advice on the following would be appreciated:

(1) I ran bootstraps and at the end of the run I saw the following error:

[2016-06-21 12:25:17.083] [jointLog] [info] wrote 99 bootstraps

[2016-06-21 12:26:10.727] [jointLog] [info] wrote 100 bootstraps

[2016-06-21 12:26:10.771] [jointLog] [info] Finished Bootstrapping

Segmentation fault

I was wondering if this is something I should be concerned about?

(2) What programs can I  use to analyze the bootstrap data? 

Thanks

[Rob]

Hi,

  A segmentation fault is usually a "bad thing®", though, if all of the output was created successfully, it should not have any effect on the results of downstream analysis.  Could you provide some extra information about exactly what version of sailfish / salmon you are using?  There was

a set of pre-compiled executables for salmon v0.6.0, with download links marked as "DEPRECATED", that were known to produce a segfault on some machines during program exit.  As I mentioned above, since this happened during program exit, none of the results were affected.  However,

we also provide a fixed pre-compiled executable version of salmon that shouldn't exhibit this behavior.


  Regarding the second question, you can use the ConvertBootstrapsToTSV.py script to produce separated files to perform any custom analysis you may want on your bootstrap samples.  Currently, there is only one downstream analysis program of which I am aware that takes this information into account when performing differential expression testing, and that is sleuth.  If you want to test out that pipeline, you'll just need to prepare the bootstrap samples for sleuth analysis; this can be done with a single function call using the wasabi package.  I have a tutorial that describes using this pipeline to analyze some data over on my blog. 

Best,

Rob