Difference between revisions of "Salmon 2016"
Schwietzer (talk | contribs) (Created page with "== Introduction == Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and s...") |
Schwietzer (talk | contribs) |
||
| (One intermediate revision by the same user not shown) | |||
| Line 5: | Line 5: | ||
Salmon is installed on the environment ''hpc-env/6.4'' in the following versions: | Salmon is installed on the environment ''hpc-env/6.4'' in the following versions: | ||
*'''Salmon/0.11.2'''-intel-2018a-Python-2.7.14 | |||
*'''Salmon/0.11.3'''-foss-2017b-Python-2.7.14 | |||
... and on ''hpc-env/8.3'': | |||
*'''Salmon/1.3.0'''-gompi-2019b | |||
== Using Salmon on the HPC cluster== | == Using Salmon on the HPC cluster== | ||
Latest revision as of 10:46, 13 May 2022
Introduction
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference.
Installed versions
Salmon is installed on the environment hpc-env/6.4 in the following versions:
- Salmon/0.11.2-intel-2018a-Python-2.7.14
- Salmon/0.11.3-foss-2017b-Python-2.7.14
... and on hpc-env/8.3:
- Salmon/1.3.0-gompi-2019b
Using Salmon on the HPC cluster
To use Salmon, you have to load the corresponding environment first and then load the desired version:
module load hpc-env/6.4 module-load Salmon/0.11.2-intel-2018a-Python-2.7.14
Documentation
If you want a short introduction to the available commands, you can use the help function after loading the module. Just type in:
salmon --help
The full documentation of Salmon can be found here.
