Seqcode
Introduction
SeqCode is a family of applications designed to develop high-quality images and perform genome-wide calculations from high-throughput sequencing experiments. This software is presented into two distinct modes: web tools and command line. The website of SeqCode offers most functions to users with no previous expertise in bioinformatics, including operations on a selection of published ChIP-seq samples and applications to generate multiple classes of graphics from data files of the user. On the contrary, the standalone version of SeqCode allows bioinformaticians to run each command on any type of sequencing data locally in their computer. The architecture of the source code is modular and the input/output interface of the commands is suitable to be integrated into existing pipelines of genome analysis. SeqCode has been written in ANSI C, which favors the compatibility in every UNIX platform and grants a high performance and speed when analyzing sequencing data. Meta-plots, heatmaps, boxplots and the rest of images produced by SeqCode are internally generated using R. SeqCode relies on the RefSeq reference annotations and is able to deal with the genome and assembly release of every organism that is available from this consortium.
Versions
1.0
Commands
buildChIPprofile
combineChIPprofiles
combineTSSmaps
combineTSSplots
computemaxsignal
findPeaks
genomeDistribution
matchpeaks
matchpeaksgenes
processmacs
produceGENEmaps
produceGENEplots
producePEAKmaps
producePEAKplots
produceTESmaps
produceTESplots
produceTSSmaps
produceTSSplots
recoverChIPlevels
scorePhastCons
Module
You can load the modules by:
module load biocontainers
module load seqcode
Example job
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run seqcode on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=seqcode
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers seqcode
buildChIPprofile -vd ChromInfo.txt \
H3K4me3_sample.bam test_buildChIPprofile