recipe splicemap

Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy.







biotools: splicemap, doi: 10.1093/nar/gkq211

package splicemap

(downloads) docker_splicemap


depends bowtie:

depends libgcc-ng:


depends libstdcxx-ng:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install splicemap

and update with::

   mamba update splicemap

To create a new environment, run:

mamba create --name myenvname splicemap

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `splicemap/tags`_ for valid values for ``<tag>``)

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