rnaseqc
salmon
rnaseqc | salmon | |
---|---|---|
1 | 1 | |
141 | 742 | |
0.7% | 1.9% | |
4.5 | 4.1 | |
about 2 months ago | 12 days ago | |
C++ | C++ | |
GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
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rnaseqc
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Tools for strand direction detection RNA-Seq
I like to use RNA-SeQC (https://github.com/getzlab/rnaseqc). It shows the percentage of forward/reverse reads that alingned to either the sense or antisense strands. It is also compatible with multiQC which is a big plus.
salmon
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Why should academic researchers use Rust?
Rust makes distribution and maintenance near trivial. My lab develops a fairly widely-used tool, salmon, for the quantification of transcript expression from RNA-seq data. This tool is written in C++14, and has a substantial number of dependencies. The process of updating the tool (e.g. bumping dependencies) and cutting a new release is painful. To maintain widespread availability, we distribute this tool using bioconda which uses it's own CI and setup to build new releases for (in our case) Linux and MacOS. Things break all the time. For example, recently, they bumped the compiler used to build packages. This changed some default "implementation defined" behavior, causing previously functioning code to fail. We didn't find this locally, because we didn't test that specific compiler version. When we tried to release a new version, we had to go back and fix things etc. This is not just because different compilers exist, but because the C++ specification is soooo complicated and the set of undefined and implementation defined behavior is sooo broad that it's very brittle and it's easy for things to "break" via bitrot. However, the stability provided by Rust has been phenomenal so far. In our code, we only use stable Rust features, and we have benefited tremendously from the empirical guarantee that valid Rust code (except in exceptional cases like latent bugs in the language) will remain valid. While not all crates follow it religiously, there is a reasonable respect for semantic versioning. Thus, cutting a new release of one of our Rust tools is often as simple as just updating the Cargo.toml (and Cargo.lock in the case of applications), tagging a new release in GitHub, and letting the bioconda CI do it's business with the tagged artifacts. The build "scripts" are almost always trivial because the builds just work, across platforms, across CIs, etc. Now, new projects like cargo dist look like they make this process even simpler.
What are some alternatives?
rnaseq - RNA-seq analyses.
TPMCalculator - TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
noson-app - The essential to control music from your SONOS devices on Linux platforms
how_are_we_stranded_here - Check strandedness of RNA-Seq fastq files
gEAR - The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
popscle - A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites
nanopolish - Signal-level algorithms for MinION data
mixcr - MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
mirdeep2 - Discovering known and novel miRNAs from small RNA sequencing data