Overview

Running on a cluster

The current implementation of the cache that GimmeMotifs uses does not play nice with concurrent access, for instance on a cluster. The result is that the cache will get corrupted and that GimmeMotifs will fail. Until this is fixed, there is a workaround. In your job submission script, use something like the following:

NEW_CACHE=$TMPDIR/cache
mkdir -p $NEW_CACHE
if [ -z $XDG_CACHE_HOME ]; then
    XDG_CACHE_HOME=$HOME/.cache
fi
cp -r $XDG_CACHE_HOME/gimmemotifs $NEW_CACHE/
export XDG_CACHE_HOME=$NEW_CACHE
echo 'Using $XDG_CACHE_HOME for cache'

This will use a local directory to store the cache.

Motif databases

By default GimmeMotifs uses a non-redundant, clustered database of known vertebrate motifs: gimme.vertebrate.v5.0. These motifs come from CIS-BP (http://cisbp.ccbr.utoronto.ca/) and other sources. Large-scale benchmarks using ChIP-seq peaks show that this database shows good performance and should be a good default choice.

In addition, many other motif databases come included with GimmeMotifs:

• CIS-BP - All motifs from the CIS-BP database (version 1.02).

• ENCODE - ENCODE motifs from Kheradpour & Kellis (2013).

• factorbook - All non-redundant motifs from Factorbook.

• HOCOMOCOv11_HUMAN - All human motifs from HOCOMOCO version 11.

• HOCOMOCOv11_MOUSE - All mouse motifs from HOCOMOCO version 11.

• HOMER - All motifs from HOMER (downloaded Oct. 2018).

• IMAGE - The motif database from Madsen et al. (2018).

• JASPAR2018 - All CORE motifs from JASPAR 2018.

• JASPAR2018_vertebrates - CORE vertebrates motifs from JASPAR 2018.

• JASPAR2018_plants - CORE plants motifs from JASPAR 2018.

• JASPAR2018_insects - CORE insects motifs from JASPAR 2018.

• JASPAR2018_fungi -CORE fungi motifs from JASPAR 2018.

• JASPAR2018_nematodes - CORE nematodes motifs from JASPAR 2018.

• JASPAR2018_urochordata - CORE urochordata motifs from JASPAR 2018.

• JASPAR2020 - All CORE motifs from JASPAR 2020.

• JASPAR2020_vertebrates - CORE vertebrates motifs from JASPAR 2020.

• JASPAR2020_plants - CORE plants motifs from JASPAR 2020.

• JASPAR2020_insects - CORE insects motifs from JASPAR 2020.

• JASPAR2020_fungi -CORE fungi motifs from JASPAR 2020.

• JASPAR2020_nematodes - CORE nematodes motifs from JASPAR 2020.

• JASPAR2020_urochordata - CORE urochordata motifs from JASPAR 2020.

• SwissRegulon - The SwissRegulon motifs.

You can specify any of these motif databases by name in any GimmeMotifs tool. For instance:

$ gimme scan TAp73alpha.fa -p JASPAR2018_vertebrates -g hg38

or

$ gimme motifs TAp73alpha.fa TAp73alpha.motifs -p HOMER -g hg38 --known