caloger/rsem-bowtie2

The docker rsem-bowtie2 can be run with the following commands:

sudo docker pull docker.io/rcaloger/rsem-bowtie2
sudo docker run -v /host/directory:/container/directory -d docker.io/rcaloger/rsem-bowtie2 sh /host/directory/reference.repository /bin/prepare_ref_bowtie2_ensembl.sh ftp.link.fa.gz ftp.link.gtf.gz n.of.threads 

The above command  is used to create the reference repository using ensembl data.

e.g:
sudo docker run -v /data/scratch/:/data/scratch -d docker.io/rcaloger/rsem-bowtie2 sh /data/scratch/hg19_bowtie2_ensembl75 /bin/prepare_ref_bowtie2_ensembl.sh ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz 24 

rcaloger/skewer1

The docker skewer1 can be run with the following commands:

For pair ends reads:
sudo docker pull docker.io/rcaloger/skewer1
sudo docker run -v /host/directory:/container/directory -d docker.io/rcaloger/skewer1 sh /bin/trim2.sh /host/directory/fastq_folder 5'adapter 3'adapter read_R1.fastq.gz read_R2.fastq.gz
e.g:
sudo docker pull docker.io/rcaloger/skewer1
sudo docker run -v /data/scratch/:/data/scratch -d docker.io/rcaloger/skewer1 sh /bin/trim2.sh /data/scratch/1864p22 GTCTCGTGGGCTCGG TCGTCGGCAGCGTC read_R1.fastq.gz read_R2.fastq.gz

Docker's images prepared by Bioinformatics and Genomics unit @ UNITO

The B&Gu is a interdisciplinary group developing tools to help Biologists to use of Next Generation Sequence Analysis tools.
As part of this aim we have developed some Docker images that can be used for basic bioinformatics analysis:

• rcaloger/demultiplexing.1, which provides bcl2fastq conversion.
• rcaloger/skewer1, which allows removal of  adapters using skewer.
• rcaloger/rsem-bowtie2, which allows RNAseq reads counts using RSEM and BOWTIE2. 
•  

demultiplexing.1

The docker demultiplexing.1 can be run with the following command:

 sudo docker pull docker.io/rcaloger/demultiplexing.1
sudo docker run -v /host/directory:/container/directory -d rcaloger/demultiplexing.1 sh /bin/demultiplexing.sh /host/directory/BCL.FOLDER Number.of.CORES 
e.g:
sudo docker run -v /data/scratch/:/data/scratch -d rcaloger/demultiplexing.1 sh /bin/demultiplexing.sh /data/scratch/160928_NB501732_0001_AHNG3GBGXY 24