TrimGalore is a wrapper tool that automates quality and adapter trimming to FastQ files. It also provides functionality to RRBS sequence files.
FastQC provides quality control checks of high throughput sequence data that identify areas of the data that may cause problems during further analysis.
These are the public key fingerprints for Owens (in hexadecimal format):
owens: ssh_host_rsa_key.pub = 18:68:d4:b0:44:a8:e2:74:59:cc:c8:e3:3a:fa:a5:3f
owens: ssh_host_ed25519_key.pub = 1c:3d:f9:99:79:06:ac:6e:3a:4b:26:81:69:1a:ce:83
owens: ssh_host_ecdsa_key.pub = d6:92:d1:b0:eb:bc:18:86:0c:df:c5:48:29:71:24:af
Perl is a family of programming languages.
Gromacs 2016.4 has been installed on Owens; usage is via the module gromacs/2016.4.
StringTie assembles aligned RNA-Seq reads into transcripts that represent splice variants in RNA-Seq samples.
Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.
HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.
TopHat uses Bowtie, a high-throughput short read aligner, to analyze the mapping results for RNA-Seq reads and identify splice junctions.
Please note that tophat (and bowtie) cannot run in parallel, that is, on multiple nodes. Submitting multi-node jobs will only waste resources. In addition you must explicitly include the '-p' option to use multiple threads on a single node.