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Hi,
I usually install subread via Conda, however the newest version (2.0.3) doesn't appear to be available there. Are there any other good options for downloading it to your personal server space or would I need to get the sys admin to install it as a module?
Best wishes,
Lucy
Hi Lucy,
We do not maintain Conda. Please check with them and they will be able to update their recipes.
We can only recommend the Rsubread package but it may not have what you are looking for.
Best regards,
Marcel
Thank you - I am looking to use featureCounts. Would you recommend the R package for this as well rather than the command line option?
The
featureCountsprogram in bothSubreadandRsubreadpackages is well maintained. I would say that any version offeatureCountsreleased in the recent years work nearly equally well in analyses, and the results should be all the same, no matter which version is used.The options related to paired-end read assignment were changed recently, hence you may need to refer to the users' manual of the version-in-use for the paired-end read related options.
Thank you, yes that was why I wanted to update the package version, but it wasn't available in Conda. I will ask my sys admin to install the new version of subread as a module.