Search Documentation

Search our client documentation below, optionally filtered by one or more systems.

Supercomputer: 

Search Documentation

Owens

These are the public key fingerprints for Owens:
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

Owens, Ruby

Perl is a family of programming languages.

Owens

StringTie assembles aligned RNA-Seq reads into transcripts that represent splice variants in RNA-Seq samples.

Owens

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.

Owens

HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.

Owens

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.

Owens, Pitzer

TAU Commander is a user interface for the TAU Performance System, a set of tools for analyizing the performance of parallel programs. 

Owens

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.

Owens

Kallisto is an RNA-seq quantification program. It quantifies abundances of transcripts from RNA-seq data and uses psedoalignment to determine the compatibility of reads with targets, without needing alignment.

Pages