docs.rail.bio

Rail-RNA v0.2

Tells you how to install Rail-RNA. You can then figure out how to use it by trial and error or try the Tutorial. Describes Rail's various outputs and how to suppress ones you don't need to save time and money. Reference. Covers command-line parameters across all of Rail's modes and job flows. Rail-RNA is a spliced alignment program: it performs intron-aware alignment of RNA sequencing (RNA-seq) data to a genome assembly. You may have heard it's designed to run in the cloud with Amazon Web Services. While...

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Rail-RNA v0.2 | docs.rail.bio Reviews

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Tells you how to install Rail-RNA. You can then figure out how to use it by trial and error or try the Tutorial. Describes Rail's various outputs and how to suppress ones you don't need to save time and money. Reference. Covers command-line parameters across all of Rail's modes and job flows. Rail-RNA is a spliced alignment program: it performs intron-aware alignment of RNA sequencing (RNA-seq) data to a genome assembly. You may have heard it's designed to run in the cloud with Amazon Web Services. While...

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3 what is rail rna

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Rail-RNA v0.2 | docs.rail.bio Reviews

https://docs.rail.bio

Tells you how to install Rail-RNA. You can then figure out how to use it by trial and error or try the Tutorial. Describes Rail's various outputs and how to suppress ones you don't need to save time and money. Reference. Covers command-line parameters across all of Rail's modes and job flows. Rail-RNA is a spliced alignment program: it performs intron-aware alignment of RNA sequencing (RNA-seq) data to a genome assembly. You may have heard it's designed to run in the cloud with Amazon Web Services. While...

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docs.rail.bio

1

Deliverables - Rail-RNA v0.2

http://docs.rail.bio/deliverables

Bed: junctions and indels. There are several classes of outputs. Each is described in a different section below. You can toggle which outputs are written with the. Job flows. By default. Tsv idx bw bed. Which is all the outputs described below besides the alignment BAMs. (Do you really need them? Suppressing the output saves a lot of space- which is especially useful on S3, where storage is rented.) If you do need BAM output, invoke. Deliverables tsv idx bw bed bam. Subdirectory of the output directory.

2

Installation - Rail-RNA v0.2

http://docs.rail.bio/installation

Setting up Amazon Elastic MapReduce. A note on security. Configuring the AWS CLI. How the installer works. Rolling your own installer. Make sure you have a recent ( = 2009) OS X or Linux box with at least 8 GB of RAM. For a no-fuss install, enter. INSTALLER=/var/tmp/$(cat /dev/urandom env LC CTYPE=C tr -cd 'a-f0-9' head -c 32); curl http:/ verve.webfactional.com/rail -o $INSTALLER; python2 $INSTALLER -m true; rm -f $INSTALLER). In a Unix shell (which you open by running the. You can visit the. This insta...

3

Tutorial - Rail-RNA v0.2

http://docs.rail.bio/tutorial

Modes and job flows. Local and parallel modes: Drosophila examples. Elastic mode: a human example. All examples in this tutorial were generated by Flux Simulator. Script from the Rail repo. We made a serious attempt to design Rail-RNA for people who don't read manuals to discourage improper use of the software. In general, you can get started by entering. In the shell. You'll obtain the following output, perhaps with a different version number. Modes and job flows. Rail-RNA has three modes- -. Or S3) fro...

4

Reference - Rail-RNA v0.2

http://docs.rail.bio/reference

X/- bowtie-idx/ idx,idx idx. A/- assembly choice tgz. Intermediate s3 dir/hdfs dir. D/- deliverables choice,. Rail-RNA is invoked by entering. Rail-rna job flow mode [args]. Job flows in succession;. To get help for a given combination of job flow and mode, enter. Rail-rna job flow mode -h. Command-line arguments (args) are described in detail below. This is the path to a Rail-RNA manifest file. Its format is described in Tutorial. FASTQ/FASTA URL (tab) URL MD5 checksum or 0 (tab) sample label. X path to...

5

dbGaP on EMR - Rail-RNA v0.2

http://docs.rail.bio/dbgap

Securely analyze dbGaP-protected data in the cloud. Set up an administrator account (administrator). Set up a new IAM user (administrator and user). Create a secure CloudFormation stack (administrator). Delegate Elastic MapReduce and CloudFormation authorites to the new IAM user (administrator). Set up default EMR roles (administrator and user). Test the configuration (user). Helpful notes for administrators. Securely analyze dbGaP-protected data in the cloud. The National Institutes of Health (NIH).

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Rail-RNA v0.2

Tells you how to install Rail-RNA. You can then figure out how to use it by trial and error or try the Tutorial. Describes Rail's various outputs and how to suppress ones you don't need to save time and money. Reference. Covers command-line parameters across all of Rail's modes and job flows. Rail-RNA is a spliced alignment program: it performs intron-aware alignment of RNA sequencing (RNA-seq) data to a genome assembly. You may have heard it's designed to run in the cloud with Amazon Web Services. While...

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