Sailfish v0.7.4 gene level summary

[Zhenhua Wu]

The new Sailfish version 0.7.4 has no genesum tool, instead, it provides a new option --geneMap. However the original "genesum" has a useful option '-k' to choose the aggregation key from the gtf file, which is not available for the new Sailfish 0.7.4. In order to do so, I have to generate a tab separated file containing transcript and gene name from the gtf file downloaded in other resources such as genecode. Is it possible to add '-k' option to allow user to choose the aggregate key in the sailfish v0.7.4?

[Rob]

Hi Zhenhua,

  I just added such an option in the latest commit.  I added an "advanced" argument --txpAggregationKey that lets you provide the name of the feature on which you want to aggregate transcript-level estimates.  Once there is a little more "feature mass", I'll roll this into a new point release as well.

Best,

Rob 

[Rob]

P.S.  If you have a compatible version of linux (compatible with ubuntu 12.04), you can get an automated build of the latest version software with this feature from here.

--Rob