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kpLogo

k-mer probability logo (kpLogo) is a probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs from a set of aligned sequences.

References:

There may be multiple versions of kplogo available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail kplogo

To select a module, type

module load kplogo/[ver]

where [ver] is the version of choice.

Environment variables set:

On Helix

Sample session:

module load kplogo

# run examples from http://kplogo.wi.mit.edu/manual.html#examples
kpLogo /fdb/kplogo/premir50p3.fa -gapped -startPos 26 -pc 0.01

kpLogo /fdb/kplogo/gRNA.txt -weighted -gapped -startPos 5 -pc 0.01
kpLogo /fdb/kplogo/gRNA.txt -ranked -gapped -startPos 5 -pc 0.01

kpLogo /fdb/kplogo/gRNA.txt -weighted -o model_training
kpLogo /fdb/kplogo/gRNA.txt -predict model_training
Interactive job on Biowulf
sinteractive

module load kplogo

# run examples from http://kplogo.wi.mit.edu/manual.html#examples
kpLogo /fdb/kplogo/premir50p3.fa -gapped -startPos 26 -pc 0.01

kpLogo /fdb/kplogo/gRNA.txt -weighted -gapped -startPos 5 -pc 0.01
kpLogo /fdb/kplogo/gRNA.txt -ranked -gapped -startPos 5 -pc 0.01

kpLogo /fdb/kplogo/gRNA.txt -weighted -o model_training
kpLogo /fdb/kplogo/gRNA.txt -predict model_training
Batch job on Biowulf

Create a batch input file (e.g. kplogo.sh). For example:

#!/bin/sh
module load kplogo

# run examples from http://kplogo.wi.mit.edu/manual.html#examples
kpLogo /fdb/kplogo/premir50p3.fa -gapped -startPos 26 -pc 0.01

kpLogo /fdb/kplogo/gRNA.txt -weighted -gapped -startPos 5 -pc 0.01
kpLogo /fdb/kplogo/gRNA.txt -ranked -gapped -startPos 5 -pc 0.01

kpLogo /fdb/kplogo/gRNA.txt -weighted -o model_training
kpLogo /fdb/kplogo/gRNA.txt -predict model_training

Submit this job using the Slurm sbatch command.

sbatch kplogo.sh
Swarm of Jobs on Biowulf

Create a swarmfile (e.g. kplogo.swarm). For example:

kpLogo sample-01.fa -gapped -startPos 26 -pc 0.01
kpLogo sample-02.fa -gapped -startPos 26 -pc 0.01
kpLogo sample-03.fa -gapped -startPos 26 -pc 0.01
kpLogo sample-04.fa -gapped -startPos 26 -pc 0.01
kpLogo sample-05.fa -gapped -startPos 26 -pc 0.01

Submit this job using the swarm command.

swarm --module kplogo -f kplogo.swarm 
Documentation