How can I check if an RNA-Seq data is stranded (strand-specific) or not?

Question

[yh1126]

How can I check if an RNA-Seq data is stranded (strand-specific) or not? Please do not recommend salmon. It is impossible to run salmon now, as it requires an outdated version of boost (libboost_iostreams.so.1.60.0) which can be installed from nowhere.

[Rob]

This is not true, on several levels. Salmon (any relatively recent version) can use any boost equal or _newer_ than 1.60. You can download the pre-compiled executable of salmon for linux here. This is statically linked, so it doesn't depend on a shared boost library. Likewise, you can also install salmon for linux or OSX via bioconda. That version automatically installs (via conda) the compatible boost. Finally, a pre-made Docker image of the latest bioconda release can be easily pulled down via docker pull quay.io/biocontainers/salmon:1.9.0--h7e5ed60_1.

[Dave Carlson]

Regarding the following:

It is impossible to run salmon now, as it requires an outdated version of boost (libboost_iostreams.so.1.60.0) which can be installed from nowhere.

What system are you on? I'm using Salmon 1.9.0 and Boost 1.74 (both installed with conda) on Ubuntu.

[Wayne]

Thanks, I also found similar in a recent installation that others can access themselves in their browser with no installation needed using the MyBinder service as detailed in comments under 'How to know that your RNA-seq is stranded or not?'.

Answer 1

[GenoMax]

This is a frequently asked question.

One recent post had many options: How to find rna strand direction before alignment?