start:software:topical:lifesciences:ngs:transcript_abundance_tools

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Assesing Transscript Abundance

Software Options

kallisto quantifies abundances of transcripts from RNA-Seq data, or more other target sequences using high-throughput sequencing reads. Modules on Mogon can be found as1):

bio/kallisto

sleuth investigates RNA-Seq transcript abundance from kallisto and perform differential expression analysis. Modules on Mogon can be found as:

bio/sleuth

Development with SeqAn3

SeqAn3 is C++ library for sequence analysis. It is a follow-up project of SeqAn2 and strives to implement efficient algorithms as a header-only library.

It provides broad functionality, can be used together with OpenMP, even MPI and relatively easy to use2).

The module for SeqAn3 is located at

lib/seqan/<version>

The older module for SeqAn23) can still be found at:

devel/seqan/2.4.0

For version 3.0.0 the following aspects apply

  • The API is not stable, yet4).
  • Loading the module will load a recent GCC and CMake.

If using CMake, be sure to include the following statements5)

set(SeqAn3_DIR "$ENV{EBROOTSEQAN}/build_system")
find_package (SeqAn3 REQUIRED)

1)
loading a module without version specification will load the most recent one
2)
provided you “speak” C++.
3)
assorted in devel because it is not only a library
4)
Presumably because the new libraries are not yet ships with STL. W.a.W.: Using the library, developing applications will likely need an adaption of include-statements, but little more.
5)
In contrast, the tutorial assumes set(SeqAn3_DIR “${CMAKE_SOURCE_DIR}/../seqan3/build_system.
  • start/software/topical/lifesciences/ngs/transcript_abundance_tools.1587044008.txt.gz
  • Last modified: 2020/04/16 15:33
  • by jrutte02