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...HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk

...Each Protospacer database is a simple catalogue of all possible Cas9 target-sites within a given FASTA sequence, i.e. all NGG/NAG sites. Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). ...